I drive a 99' manual transmission 4WD with 231K.

3 months ago I had trouble shifting into 4th while cruising around 50mph and ended up accidentally grinding it in 2nd for a brief moment and once I had it secured in 4th the RPM's spiked up for a few seconds with no boost in acceleration and I instantly began worrying about the clutch, but experienced no more issues for months.

Driving up a mountain pass today the RPM's started jolting up while I would lose acceleration briefly and on the steepest section I eventually didn't have enough acceleration to continue at all. I managed to turn around and coast way down the mountain, but while engine braking in 1st gear running the RPM's low I heard a clunk like I hit a bump and acceleration was gone for good after that. In hindsight I wish I hadn't overestimated what was left in the clutch and just left it in neutral, tapping the brakes the whole way down, which I had to do anyway, but the road was icy and I was trying to play it safe.

I coasted for miles and rolled it into the nearest auto shop parking lot and now I'm debating whether I want to take on this replacement myself or just bite the bullet and hire the shop for it. I'm worried what damage the engine braking might have caused outside of the clutch assembly... damage I might overlook while down there.

I read this write-up and skimmed the links to the others on the topic: Clutch Replacement Writeup

It seems the additional tools I'll need to get ahold of include a snap-ring wrench, torque wrench, transmission jack, maybe a seal driver, and the parts obviously.

But I have a few questions based on issues mentioned in the write-ups:

1."Once all that is done you can start the joy of unbolting the transmission. All 6 bolts are 17mm. To get the very top one I used a universal, two longer extensions and one short extension. I held the socket on the bolt from the passengers side and ran the extensions up the drivers side. Once I had the socket on and a little pressure I could take my right hand off the socket and put some torque on the ratchet."

Does anyone know what length in extensions is needed to reach this furthest top bolt?

2. "The rear main seal came out using a hooked pick. Started on the inside of the seal (closest to the crank), pushed it through, then rotated it behind the seal and pulled out. I had seen some information on these a few other times which mentioned that Toyota changed their part and the new one is slightly smaller than the old in thickness (space it will occupy from the motor towards the rear of the vehicle). I checked and sure enough it was. This was the joy in why IÂ’ve done the job three times. I had blocked crankcase ventilation which was putting too much pressure on the seal and pushing it out. I guess having to work on the RMS a few times is a better way of discovering the issue than some sort of major failure. Anyways, for reinstallation I pushed the seal all the way until flush with the seating surface of the engine (i.e. the retainer plate), which meant the crank stood slightly proud."

So with the size difference between new and old rear main seals. the solution is to push the seal flush with the retainer plate and it's good to go? Anyone else experience issues with replacing this that they can share about?

3. In the past I've replaced the rear axle seals and rear differential gasket with 4Runner lifted on regular jack stands. Seeing as the transmission has to be lowered. Would ramps or heavy duty truck jack stands be best for this job?

I'll be doing this job at some point so I have been saving up links. Here are a bunch:

Clutch replacement - double check & advice

Anything I should think about replacing while the Trans is out?

3rd gen 5vz AISIN clutch nightmare F-up

Clutch Replacement

99 5 Speed Clutch Replacement Advice Needed

Clutch replacement in the near future

And @sae10w30 was nice enough to send me a write-up of the steps he took to do his which I'll copy below:

Tools:
. 30 inches of 1/2-inch socket extension bars (16" bare minimum)
. At least one U-joints and swivel joint
. Snap-ring https://youtu.be/9UmrCl2nLKM?t=142pliers (for the transmission case snap ring)
. Gear puller
. Torque wrench & sockets (all 1/2 inch sized)
. Note that the 4-cyl ten 14mm flywheel bolts are 12 point (not 6 point)

Fluids:
. 2.7 quarts replacement 75W90 GL4 gear lube
. Thick high-moly graphite grease to lube the spline input shaft
. Thick high-moly graphite grease to lube the ID of throwout bearing
. Toyota FIPG for the rear main seal (RTV is ok but not as good)
. No grease on diaphragm springs, pressure plate or throwout bearing face.
. Light grease on throwout bearing ID, input shaft splines
. Light grease on clutch fork pivot points & outside the shaft collar

Torque specs:
http://www.ttora.com/forum/attachmen...1&d=1509155312
. Starter bolts 30ft#
. Bellhousing bolts 54ft#
. Flywheel (either 19 ft lbs+1/4 turn for 3RZ or 65ftlbs for the 2RZ & 5VZ)
. It is said that the two torque methods above result in the same end torque.>
. Pressure plate bolts ?

Rockauto Aisin Kit CKT-051:
. Aisin disc stamped DTX-137L & 6H26
. Aisin diaphragm stamped Aisin 17.01.20 & CTX-106
. Koyo pilot molded 6201 RS ROM 017 & Koyo 6201 RS ROM 057
. Koyo pilot box printed 6201RSC3 & PBT-002
. Koyo release stamped Koyo Japan 49H & RCT356SA9
. Koyo release box printed RBT-004 & RCT356SA9 & FG Gen M1412
. Plastic alignment tool stamped USA 11

Before:
. Check/measure before/after clutch pedal free play
. It should be 1/4" to prevent throwout bearing wear

Shifter Assembly:
. Chock rear wheels and set parking brake
. Unscrew shifter knob (counterclockwise)
. There is no need to loosen or remove either side brown plastic garnish
. Don't remove the brown plastic garnish on either side - just leave it
. Pry up the front of the black ashtray (it has a clip on each of the 4 corners)
. Pull out on the driver side garnish
. At the same time, pry up on the ashtray toward driver side door
. That should remove the black ashtray from all four corner clips
. With a P2 Phillips or 10mm socket, remove 4 rectangular-plate screws
. Pull up on the boot until it stops about halfway up on the shaft
. Don gloves and use a 1/8" flathead scewdriver for force
. Press down hard on the inner ring of the shiftlever cap
. Use the screwdriver as a pushrod & rotate the cap 1/8 turn counterclockwise
. This will pop it out
. Remove the cabin gear shift mechanism
. While above, snap pictures of the pitch-fork-shaped wiring harness from above
. http://www.showstop.org/images/misc/r150F-harness.jpg
. If possible, unbolt the "conning tower" for the shift mechanism

Photo electrical connections:
. While the 4Runner is on the ground, put the transmission in the top gear
. 10mm socket disconnect the battery negative cable (for starter bolts removal)
. 4x-jackstand the car as high as you can get it
. Attempt to level the vehicle so the engine is level with the trans
. While below, snap pictures of the pitch-fork-shaped wiring harness
. Notice the passenger side oxygen sensors & the speedometer
. Notice the driver side reverse sensor
. Notice the three main harness clips on the top of the transmission

Drain fluid:
. Loosen both the 24mm fill plug & 24mm drain plug
. Drain the Red Line MT-90 80W90 from the 24mm drain plug

Remove driveshaft:
. Mark the alignment on both ends of the driveshaft
. Remove four the rear-facing drive shaft 14mm bolts
. Twist the drive shaft with the parking brake off to access the bolts
. Pull the back end down & pull driveshaft out of the transmission

Remve slave cylinder:
. Remove 2x12mm bolts for the clutch slave cylinder
. Hang clutch slave cylinder safely on hangar wire if necessary

Disconnect exhaust pipe bracket:
. Don't remove the exhaust pipe (leave the pipe)
. Remove 17mm bolts holding exhaust pipe bracket to transmission housing
. This isn't needed: Remove 12mm bolts holding exhaust pipe into the bracket
. Do not separate the exhaust pipes (most seem to say).

Remove passenger side wiring harness connections:
. Remove 1x12mm bolt holding the upstream O2 sensor bracket
. Remove 1x12mm bolt holding the speedometer in place
. Put a pan under the speedometer to catch inevitable drippings
. Wiggle and pull out the three-screw plastic speedometer sensor

Remove driver side wiring harness connections:
. Remove 1x12mm bolt holding harness next to the fill plug
. Loosen (do not remove) 1x1-1/16 bolt holding reverse sensor
. It's impossible to twist off the reverse sensor so don't try!
. Twist reverse sensor 180 degrees to access clip connection
. Press the clip connection to disconnect the harness from the sensor

Remove the 3 main harness connectors on top of the transmission:
. (Access all three from the driver side using socket extensions)
. Remove the 14mm harness bracket bolt at the bell-to-engine line
. Remove the 10mm harness bracket bolt at the bell-waist line
. Remove the 14mm harness bracket bolt at the trans centerline
. From below, fish the loose harness into the shift lever opening
. From above, wire hanger the harness to the steering wheel

Remove the starter housing bolts:
. Remove the two 14mm bolts holding the starter to the bell housing
. Remove the lower 14mm bolt that holds the brake line & a harness connector
. You can't easily get to that bolt from the wheel well or from underneath
. You can remove the driver side wheel to put a flashlight on the upper bolt
. Then remove that upper 14mm bolt from above with just a socket and handle
. The starter motor will fall down of its own weight so tie it securely

Remove the bellhousing bolts (count all seven!, plus 2 for the starter):
. Start with bottom bolts before you place the transmission jack in the way
. Then do the upper bolts, once the transmission jack is in place.
. 1st remove the forward facing 14mm bolt & nut at the 5:30 bell housing position
. 2nd remove the forward facing 14mm bolt & nut at the 7:00 bell housing position
. 3rd remove the rearward facing 14mm bolt at the 6:30 bell housing position
. 4th remove the rearward facing 14mm bolt at the 3:30 bell housing position
. Then remove the engine-facing plate covering the lower half of the bell housing
. 5th (just in case) remove the forward facing 12mm bolt at the 11:00 bell housing position
. This bolt holds some sort of cooling or vacuum lines the back of the engine
. 6th remove the forward facing 17mm bolt at the 9:30 bell housing position
. Access that bolt from underneath using a sockt + short swivel + 3" extension
. 7th remove the forward facing 17mm bolt at the 11:30 bell housing position
. Access that bolt from the rear of the transmission behind the crossmember
. I used about 30 inches of 1/2-inch socket extensions (no swivel needed)
. 8th remove the forward facing 17mm bolt at the 12:30 bell housing position
. I used about 30 inches of 1/2-inch socket extensions (a swivel was needed)
. I used about 30 inches of 1/2-inch socket extensions (a swivel was needed)
. I used a 17mm impact socket + 5" swivel + 10" + 6" + 10" + 3" half-inch extensions
. I first tried 3/8" extensions but they simply twisted given the force
. It's still useful to have 3/8" extensions for non-torque removal & reassembly
. I used a 17mm socket + 6" swivel + 24" + 6" three-eights-inch extensions

Check that everything is out of the way:
. Zip tie any cables in place so that they don't get damaged later
. Then support the transmission with a transmission jack or jack saddle
. It is said that the rear will be slightly lower than the front for the jack
. Strap the transmission in but rout the straps under any wires

Disconnect the rear of the transmission:
. Remove the 12mm & 14mm bolts holding the rear transmission mount assembly
. Tip the front down an twist the front of the transmission to the driver side
. Pull out straight where the shaft must be aligned & the dowels stick sometimes
---------- here is where I am now so the rest is light on details ----------
. Keep the straps loose until you pull away and then tighten the straps
. Lower the transmission (by hand is ok if you can)
. Mark the drive shaft to the crank shaft alignment with a sharpie
. Flywheel bolts will require an impact driver almost certainly.

Disassembly:
. Don't breathe the dust
. Use a star pattern to remove 12mm bolts holding clutch onto bell housing
. Snap pictures of the asymmetrical nature of the clutch disc before removing!
. (It is said the Toyota 3.4L V6 engine has the disc springs toward the flywheel)
. (It is said the Toyota 2.7L I4 engine has the disc springs toward the trans.)
. (The springs go toward the pressure plate.)

. Remove the clutch disc
. Remove the pressure plate (bolts?)
. Remove the ten (12-point) 14mm bolts ringing the flywheel to the engine
. Have the flywheel replaced or resurfaced
. Remove the flywheel pilot bearing with a bearing puller
. (reassembly supposedly being the reverse of removal)

Alignment pins:
. Consider picking up exact bolts but 2 to 3 inches longer
. Cut off the heads, and saw a screwdriver channel
. Use them as alignment pins when replacing
. Notice the steel dowels between the engine & transmission

On reassembly (which most DIYs ignore), these topics came up in other DIYs:
. A screwdriver wedged into the flywheel teeth immobilizes it for tightening
. It is said that so does a punch through one of the flywheel holes
. Consider the wiring harness layout while lifting the transmission back
. Be in 5th gear when aligning splines (allows output & input shaft to turn)
. Input shaft alignment stage 1 is getting splines to go into the clutch disc.
(Time 142 seconds on [URL="https://youtu.be/9UmrCl2nLKM?t=142"]
shows the alignment problem.)
. Input shaft alignment stage 2 is the last inch onto the input shaft bearing
. Jack fine tuning matters last inch (use bellhousing bolts as alignment pins)
. It is said the bellhousing has an alignment dowel near the slave-cylinder mount
. It is said to grease the top & inside of the clutch fork ends
. Grease the adjoining surfaces
of the "throwout bearing" (also sometimes called the "release bearing").
. Grease the divot in the middle of the clutch fork
. Just before you install the clutch slave cylinder (aka "release cylinder"),
grease the divot at the end fork
. Cover the clutch fork mushroom bolt with HD grease

DIY 5VZ
http://www.ttora.com/forum/2-early-t...lutch-job.html
http://www.4x4wire.com/toyota/4Runne...enance/clutch/
http://www.toyota-4runner.org/3rd-ge...t-writeup.html
.
3RZFE:
http://www.toyota-4runner.org/3rd-ge...ck-advice.html