Wiring diagrams are not hard for me to read since my other hobby is vintage audio. I know its quite a bit different from automotive but EWDs are EWDs. The hard part for me is locating components on the vehicle.

The ECUs are exactly the same except the ST1. How did you find out what it is? If you have a diagram please post it!

I don't have to press on the brake to start the vehicle, it starts either way. Maybe thats why my 4Runner doesn't have it. Well I don't think it should cause any trouble if nothing is coming to that pin???

I think I found a diagram in another thread on how to wire that switch to the manual tranny. I don't think my wires would be the same colour since Toyota loves to change wire colours))) I think I can figure it out by the pin numbers from the switch. Diagram attached bellow.

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wiring diagrams for me are like theoretical math equations, sure I recognize the numbers but the concept is sailing way over my head.
Click on the link TheDurk gave you and scroll all the way to the bottom, that is where the wiring diagram for your 2002 runner is. It shows ST1 on the ECU. I do not have one for a 2004 tacoma so I cannot help you there. I also cannot help you much with that diagram for the park neutral switch because I replaced the engine wiring harness when I did my swap. That gave me the proper wires for the transmission. Just concentrate on what the 2004 tacoma ecu needs and make sure all the pins are in the right place. The p/n get replaced with the clutch start and the reverse needs to get wired in. You can put the reverse switch on the manual tranny and wire it that way. Pull off the glove box on your runner( just a couple bolts) and you can see the ecu and all the wiring for it

Theres one connector with 2 wires on the manual tranny, I was assuming its the same on the auto tranny for the reverse lights.

I'll look through those diagrams again.

The reverse lights in the auto are in the park neutral safety switch which you won't have any more. You can either jump it like in the diagram you posted or use the switch in the manual trans and wire it yourself. Think about replacing the whole engine wiring harness from the 2004 tacoma if you have access to one, It takes about three hours to do and comes with everything you need for the manual transmission( you will need a upper manifold intake gasket) and is guaranteed to have the proper pin placement on the ecu.

Unfortunately I don't have access to a harness. I'll try to make my harness work first.

I'm cleaning up the wiring mess under the dash right now. Just looking at the ABS/VSC computer and can't figure out where to put it since its bolted on in the exact spot where the clutch pedal is suppose to go. I wonder if I unplug it for now, can I drive without it? Or my brakes would be gone completely? I really don't want to extend the wiring for it and fish it through to the other side of dash.

I'm pretty sure there is something very different between Tacoma's and 4runners in ecu and ENGINE harness.

Probably not as much as you might think. It is the same engine whether it is in a 4runner or tacoma or tundra. Same requirements to run it. The bigger differences are between auto and manual and early and later drive by wire. As long as the tacoma ecu has every wire correctly met it should work. Of course the devil is in the details and the OP has volunteered to be the one to find out

I wanna say the egr are different. I'm not 100% sure. A good source for this is yotatech

As I've mentioned before, I checked every wire function on both and they are exactly the same.

Now today I've found out that not many 04 Tacos came with VSC/TRAC, it was an option and many trucks were made without it, I think more than with it. The ECU I ordered from a salvage yard in another province is from 04 Taco but it's a mystery whether it had VSC or not. My other thought is that Toyota may have made the ECUs the same whether it had VSC or not since it came as an option. I guess we'll find out when I plug it in)

Now I'm trying to find out where the VSC computer is mounted on those Tacos. I think I'll have to ask on the Taco forums.

The auto tranny is out. Tcase bolted right up to the manual. Forgot to order bolts for flywheel and pressure plate. Getting them tomorrow and its going in. The interesting part would be all the wiring, I'll keep you posted on how it goes.

The tranny is in and everything else is completed. It drives fine, reverse lights work, clutch safety works as well. The wiring was done the same way as the rest of the threads, just used the diagram I posted above. The wire colors are different but pinouts on the PN switch plug are same.

I'm not going to go into detail on the whole swap since its been pretty much covered a few times before. The point of this thread is the CEL and ECU issue since its a 02 4Runner.
The ECU from 2004 Taco was plug and play and the most important NO CEL! I'm getting the VSC TRAC OFF lights though. From what I found out VSC and TRAC are a very rare option even on 04 Tacos so I'm guessing my ECU is not set up for it. Oh well, I'm not too worried about it since there wasn't a time where either one came in handy, TRAC may have been useful for helping to get out of a ditch but I think I can do without. I'm just going to take the bulbs out of the cluster and forget about it.

The VSC computer is still needed though since it controls ABS and the brakes, I tried running without it and barely stopped, the brake pedal was like a rock))). The module can be hidden under the lower dash panel and the mounting points have to be cut off from the housing.

Now I'm a happy owner of a 2002 5-speed!) it feels cool since not many people get to drive the same vehicle with auto and manual tranny)

It is a great feeling isn't it? Awesome sauce on figuring out the cel. I'm ready to pull the bulb out of mine since I have the ultra Guage to monitor it anyways.

I'm totally impressed. I have an 02 with failing transmission. I have always wanted to do this. The ECU was the only problem. I'm going to start preparing to do this now before it fails.

I must have missed when you posted after you finished. Great! Now you have a pretty unique vehicle and the manual is a lot more fun to drive. Thanks for posting the result for others to use

So after a night of thinking about this.

Since the 2004 Tacoma ECU didn't solve the CEL problem, we may as well stay with our 02 ECU and wire in resistors that match the shift solenoids resistance etc. to trick our ECU into thinking the auto is there. Then you would not have to remove the CEL bulb at all nor would you have to buy a 2004 ECU. But on the other hand, if you could find a 2004 Tacoma ECU with VSC that would be ideal. Did you ever find out if there is a different part number for that one?