Transmission Musical Chairs - Q and A for those who have swapped Auto and 5spd's

[12BYotaFan]

To simplify a long story: I have a '99 sr5 with an automatic. I purchased my parents "spare beater," which is a '98 sr5 5spd 4wd because the frame has rusted out from under it. IT's powder that crumbles in your hand. My sister has a '97 with a good frame and body/interior/engine, which ate the front pump. I want the 5spd, my sister needs a new automatic.

So, I am going to have some transmissions swapped around.

The main swap, which I will be having my local transmission shop do (I'm working 75-sh hours a week) is the 5spd into my '99.

I have a complete donor vehicle, less the crossmember, which my auto-cross member will have to be modified to work. The 5spd's crossmember is... cancer riddled.

1) Do I absolutely need to swap ECU's and engine wiring harness, and re-pin the body harness to work with the '98's ECU?

I cannot have CEL's when inspecting the vehicle.

2a) I have seen it suggested that one can simply measure the resistance of each shift solenoid, and wire in resistors into the plug so that the automatic's ECU continues to function as if the automatic were there.

2b)Then to wire in a jumper up to the clutch cancel switch (from donor vic) to the neutral safety switch lead, so that the ECU will read neutral and you can start the engine (with/w/o the clutch).

2c) Then of course wire the 5spd's reverse switch into the reverse circuit of the automatic transmission plug.

If that is all that is needed to keep the original automatic ECU happy and CEL free, then I am good to go. I can move the transmission plug up into the center console to keep it accessible, and keep rolling.

Both the '98 and '99 are Sr5's, and do not have the "on the fly" center locking transfer case.

I am hoping that I also do not run into a situation where my crankshaft is not machined to accept the pilot bearing. I have seen in multiple threads that this is an issue "with certain model years" but I have not seen a reference to a thread where someone has had this issue, or a reference to any information on how to see if your engine can be verified as having a crank with a pilot bearing prior to the teardown. Can anyone provide any insight to this? Any personal experience or links to threads where this has occurred?

I know the maintenance history of my '99's engine. I would be very wary of swapping in the '98's engine, as that would force an ECU and engine bay wiring harness swap, and I believe there are differences between the 98 and 99 model years for the plugs that connect the engine harness and body harness into the ECU (and also not sure that it would just come down to repinning the existing body harness into older plugs and it all being hunky-dory).

I am trying to keep things as Original and minimally modified/hacked together, with as few changes to the wiring harness as possible, to prevent future headaches.

---

The next issue is the difference in plugs between the '99's automatic and the '97's harness plug. From what I have referenced so far, the same wiring should be present, but the plug and colors will be different.

3)I should be able to buy the newer harness plug through toyota and repin, based off the service manual reference for each model year, correct?

Threads/Posts I am referencing:

Post #26 in this thread, for automatic plug jumper. Extrapolating that his wiring changes were enough to get him back on the road and starting/driving correctly.
https://www.toyota-4runner.org/3rd-gen-t4rs/105258-5spd-swap-here-goes-nuthin-2.html

Frontrange 4x4 3.4 and 5spd swap to 2nd gen's, so not 100% applicable.
TOYOYA INFORMATION AND LINKS - Page 3


2002 Double Cab 5-Speed/4x4 Conversion - Page 5 - TTORA Forum

Any and all help and answers/references, is Greatly Appreciated!

 

[St Runner]

Your biggest issue to swap the 98 5speed into your 99 is going to be the wiring. Mechanically it should not be a problem and all the parts from the 98 will work. My personal advise would be to find a used ecu from a 99 manual along with the engine harness, If my internet reading is correct it should be plug and play with just the addition of wiring for the clutch starting circuit. Even though the crossmember is rotten make sure the the transmission mount is kept and used as it is different from the auto

 

[12BYotaFan]

@ St Runner

Is an ECU and harness swap completely necessary though? If the harness can be made to work without it, I would prefer not to have to swap. It's about trying to avoid the snowball effect of disconnecting 20 year old plastic connectors, if possible. And then I'm not sure if the replacement ECU would cause problems with the security system? Isnt there a lockout to prevent stolen parts from being used?

Again, if I can keep the original harness and ecu, that would be greatly preferred. I can pull/extend the auto.tranny's harness up into the dash to protect it and tie my wiring in. I just need to know if this is viable, if anyone has done this, or seen it done, and what the result was, as far as driveability, CELs, etc.

The other issue is that I would need to find an ecu from a '99 5spd with california smog. The '98s only federal smog, unfortunately, so **If** I run into the situation where the crank doesnt accept a pilot bearing, then an engine and ecu swap must occur as well, and the exhaust system. And I'm not sure if I will run into problems at that point, if my vehicles vin comes up as cali smog compliant, but is equipped only for fed.smog, when it comes time for inspection.

 

[Team_Jake]

See my replies in red, I just did a 5-speed swap in my '99:

To simplify a long story: I have a '99 sr5 with an automatic. I purchased my parents "spare beater," which is a '98 sr5 5spd 4wd because the frame has rusted out from under it. IT's powder that crumbles in your hand. My sister has a '97 with a good frame and body/interior/engine, which ate the front pump. I want the 5spd, my sister needs a new automatic.

So, I am going to have some transmissions swapped around.

The main swap, which I will be having my local transmission shop do (I'm working 75-sh hours a week) is the 5spd into my '99.

I have a complete donor vehicle, less the crossmember, which my auto-cross member will have to be modified to work. The 5spd's crossmember is... cancer riddled.

The cross members are the same between A/T and M/T, it's the cross member mount that is different, be sure to get the M/T cross member mount and use your original cross member.

1) Do I absolutely need to swap ECU's and engine wiring harness, and re-pin the body harness to work with the '98's ECU?

You should absolutely swap your ECU unless you want to have a wiring nightmare. Do NOT use the '98 ECU though. Get the correct ECU, it's plug and play and no re-pinning is required.

I cannot have CEL's when inspecting the vehicle.

2a) I have seen it suggested that one can simply measure the resistance of each shift solenoid, and wire in resistors into the plug so that the automatic's ECU continues to function as if the automatic were there.

If you get the correct M/T ECU you don't have to worry about this.

2b)Then to wire in a jumper up to the clutch cancel switch (from donor vic) to the neutral safety switch lead, so that the ECU will read neutral and you can start the engine (with/w/o the clutch).

All you NEED to do is jump the wires connecting pins 5 and 6 and it will start and run. If you want to wire everything correctly it will take a little more work.

2c) Then of course wire the 5spd's reverse switch into the reverse circuit of the automatic transmission plug.

Correct.

If that is all that is needed to keep the original automatic ECU happy and CEL free, then I am good to go. I can move the transmission plug up into the center console to keep it accessible, and keep rolling.

Both the '98 and '99 are Sr5's, and do not have the "on the fly" center locking transfer case.

Doesn't matter in a 5-speed swap.

I am hoping that I also do not run into a situation where my crankshaft is not machined to accept the pilot bearing. I have seen in multiple threads that this is an issue "with certain model years" but I have not seen a reference to a thread where someone has had this issue, or a reference to any information on how to see if your engine can be verified as having a crank with a pilot bearing prior to the teardown. Can anyone provide any insight to this? Any personal experience or links to threads where this has occurred?

I haven't heard of this in the 5VZ engines, you should have no problem. The pilot bearing fit just fine in my '99.

I know the maintenance history of my '99's engine. I would be very wary of swapping in the '98's engine, as that would force an ECU and engine bay wiring harness swap, and I believe there are differences between the 98 and 99 model years for the plugs that connect the engine harness and body harness into the ECU (and also not sure that it would just come down to repinning the existing body harness into older plugs and it all being hunky-dory).

Way too much work, the M/T will mate just fine to your engine.

I am trying to keep things as Original and minimally modified/hacked together, with as few changes to the wiring harness as possible, to prevent future headaches.

---

The next issue is the difference in plugs between the '99's automatic and the '97's harness plug. From what I have referenced so far, the same wiring should be present, but the plug and colors will be different.

Again, just get the correct M/T ECU and you won't have to worry about any wire harnessing. The '99 A/T and M/T ECUs are plug and play.

3)I should be able to buy the newer harness plug through toyota and repin, based off the service manual reference for each model year, correct?

Threads/Posts I am referencing:

Post #26 in this thread, for automatic plug jumper. Extrapolating that his wiring changes were enough to get him back on the road and starting/driving correctly.
5spd swap, HERE GOES NUTHIN!

Frontrange 4x4 3.4 and 5spd swap to 2nd gen's, so not 100% applicable.
TOYOYA INFORMATION AND LINKS - Page 3


2002 Double Cab 5-Speed/4x4 Conversion - Page 5 - TTORA Forum

Any and all help and answers/references, is Greatly Appreciated!

If you need a little reference as to what to do, take a look at my build thread. This is not a hard job and there were no real surprises other than the immobilizer issue I was having, but that got resolved quick.

 

[huski]

When i did my swap in my 99 limited i did exactly what you're talking about with resistors and the harness jump. It worked fine with the auto ecu but ended up throwing a code for p1780.

I ended up solving that by wiring in my clutch pedal position switch to tell the ecu when its in park,neutral, and drive. It takes a bit of doing but it is possible. I'll see if i can dig up my wiring diagrams.

A clever way to give yourself more time is you could get the vehicle inspected for a year, do the swap and figure out the wiring as you have time.

 

[St Runner]

A 99 manual ecu will make everything work correctly and save you a ton of time and effort figuring out any difference between the 98 and 99. They changed a lot between 98 and 99 but mostly in subtle ways. Any difference in sensors or wiring has to get figured out by schematics or worse, trial and error. Its a lot of work. A 99 manual ecu is what your car will be so everything will work correctly. The body harness plug should fit right into the manual ecu correctly unlike the earlier models that had different plugs for auto and manual. I suggested the wiring harness mostly because the earlier models were a lot different between auto and manual. Its possible that on the 99 they are similar enough you might not need to. If you don't you will still need to figure out how to run the reverse lights off the park neutral switch. Two hours installing the 99 manual wiring harness takes care of that. The security system is not run from the ecu which is almost completely engine management, so there will not be a problem there. The biggest difference between the auto and manual is how the starting circuit is run so that will need to get figured out regardless of how you go about this

 

[St Runner]

After rereading i realized its just the transmission from the 98 so you don't have to worry about the differences in years. I am still going to recommend the 99 manual ecu as it will make not throwing an engine light much more of a sure thing. All that info for the auto transmission will not be there and the ecu is looking for it so you either have to fool the ecu or change out the ecu. Not easy to find a cali manual though

 

[12BYotaFan]

@ St Runner

Thank you for the response. I will search for a '99 cali smog 4x4 mt ecu. In the meantime, I will risk the wiring harness headache. Do you happen to know if the harness is also required (again, snowballing from aged connectors), or can some pins be removed from the A/T harness for the m/t ecu? Worst to worst, I have 9 more months to find an ecu. (Admittedly, there is nothing more permanent than a temporary fix that works.)

You did mistake my last question about repinning my 97's harness to work with the automatic from my '99. The 97 is a federal smog, I dont think it would be wise to try to swap ecu and harness from my cali smog 99 into it. I'm just trying to salvage my parents/sisters spare vehicle because the frame/body/interior are still in decent shape. It had a transmission whine for Years and years before it bit the dust.

I purchased a new transmission mount for a '98 mt, good to hear that the crossmember itself is the same.

Like I said, musical chairs, lol.
[MENTION=145817]huski[/MENTION]

If you can point me in the direction of how you did that, I'd be grateful. I need this vehicle driveable. I already get questioned for my abs light, even though an abs light doesnt disqualify you from passing inspection here in PA. I plan to put the abs fuse on a switched relay so that I can re-enable it if it becomes a problem in idaho. For now I just have the fuse yanked.


As far as replacement parts go, I have a new master cylinder for the clutch, I replaced the slave cylinder about a year/2500 miles ago, so it will be reused. New clutch kit, bearings and all. And then everything else can be pulled from the donor vic. New output shaft seals for the transfer case. New u-joints for the driveline, excepting the doublecardan (which I checked, it has no play in any direction and the seals seemed ok).

 

[Team_Jake]

Do you happen to know if the harness is also required (again, snowballing from aged connectors), or can some pins be removed from the A/T harness for the m/t ecu?

The wiring harness is not required, just use your old one. There are 4 total plugs that plug into your A/T (the speed sensor connector, solenoid connector, ATF temp connector, and P/N position switch). Cut the P/N position switch wires and re-wire with your reverse lights, clutch pedal switches, and clutch start cancel switch, the other plugs to the A/T can just remain unconnected (or if you want to be safe you can cut & cap those wires or just tape all the plugs like I did so no dirt gets inside them and causes a short).

 

[anniesball72]

That is exactly how I did it on my 2002. Passes smog no problem

 

[anniesball72]

@ St Runner

Thank you for the response. I will search for a '99 cali smog 4x4 mt ecu. In the meantime, I will risk the wiring harness headache. Do you happen to know if the harness is also required (again, snowballing from aged connectors), or can some pins be removed from the A/T harness for the m/t ecu? Worst to worst, I have 9 more months to find an ecu. (Admittedly, there is nothing more permanent than a temporary fix that works.)

You did mistake my last question about repinning my 97's harness to work with the automatic from my '99. The 97 is a federal smog, I dont think it would be wise to try to swap ecu and harness from my cali smog 99 into it. I'm just trying to salvage my parents/sisters spare vehicle because the frame/body/interior are still in decent shape. It had a transmission whine for Years and years before it bit the dust.

I purchased a new transmission mount for a '98 mt, good to hear that the crossmember itself is the same.

Like I said, musical chairs, lol.

[MENTION=145817]huski[/MENTION]

If you can point me in the direction of how you did that, I'd be grateful. I need this vehicle driveable. I already get questioned for my abs light, even though an abs light doesnt disqualify you from passing inspection here in PA. I plan to put the abs fuse on a switched relay so that I can re-enable it if it becomes a problem in idaho. For now I just have the fuse yanked.


As far as replacement parts go, I have a new master cylinder for the clutch, I replaced the slave cylinder about a year/2500 miles ago, so it will be reused. New clutch kit, bearings and all. And then everything else can be pulled from the donor vic. New output shaft seals for the transfer case. New u-joints for the driveline, excepting the doublecardan (which I checked, it has no play in any direction and the seals seemed ok).

You can also use Tacoma ECM

 

[12BYotaFan]

@ anniesball72 were you referring to Team_Jake's post? Do you have any CEL's or codes at all?

You said you can also use a Tacoma ECU. That's good to hear, I've been searching car-part.com, alot of the postings state "'99 4wd m/t cali smog" and then come up as different model years or A/T ecu's when selected.

 

[Team_Jake]

OP, the ECU part number you want is 89661-3D590, but they are very difficult to find. This is the one I have, I found mine through another member who found one in a salvage yard. Other ECUs might work, like the 2000 model year 89666-35160, from what I understand everything powertrain-wise is exactly the same and the ECU pin connectors are the same so it should work, but 89661-3D590 is a sure bet.

There was no CA spec 1999 Tacoma, but there was a CA spec 2000 Tacoma, and the ECU part number is 89661-04670. If you look at the pin connectors on the ECU, the connectors are all the same except the middle connector, which is missing from the Tacoma ECU. All the wires that ran off that middle connector are for an immobilizer system, so if your 4Runner came with the factory immobilizer then this ECU will NOT work, but if you don’t have the factory immobilizer I don’t see why this ECU wouldn’t work.

After all this, you CAN run with your A/T ECU and it’ll drive just fine but with a CEL, and just keep your eyes peeled for the proper ECU before you do a smog check...one will pop up for sale every once-in-a-while.

 

[anniesball72]

OP, the ECU part number you want is 89661-3D590, but they are very difficult to find. This is the one I have, I found mine through another member who found one in a salvage yard. Other ECUs might work, like the 2000 model year 89666-35160, from what I understand everything powertrain-wise is exactly the same and the ECU pin connectors are the same so it should work, but 89661-3D590 is a sure bet.

There was no CA spec 1999 Tacoma, but there was a CA spec 2000 Tacoma, and the ECU part number is 89661-04670. If you look at the pin connectors on the ECU, the connectors are all the same except the middle connector, which is missing from the Tacoma ECU. All the wires that ran off that middle connector are for an immobilizer system, so if your 4Runner came with the factory immobilizer then this ECU will NOT work, but if you don’t have the factory immobilizer I don’t see why this ECU wouldn’t work.

After all this, you CAN run with your A/T ECU and it’ll drive just fine but with a CEL, and just keep your eyes peeled for the proper ECU before you do a smog check...one will pop up for sale every once-in-a-while.

Yes! that is all true. In my case I am running a 2004 MT Tacoma because there was not a MT offered in a 4Runner in 01-02. I pass smog with no problems.

Basically like stated. As long as the pin outs are the same you shouldn't have a problem.

 

[anniesball72]

@ anniesball72 were you referring to Team_Jake's post? Do you have any CEL's or codes at all?

You said you can also use a Tacoma ECU. That's good to hear, I've been searching car-part.com, alot of the postings state "'99 4wd m/t cali smog" and then come up as different model years or A/T ecu's when selected.

No CELS! And yes I was referring to Team_jakes post.