1997 5 speed manual 4Runner. Clutch pedal is soft and won't fully engage after resting overnight after long multi-hour drives. But is perfect otherwise.

Just had the following done:

Transmission taken apart inspected, parts replaced by a really good shop that specializes in this and ships nationally.

New Excedy clutch installed. Hydraulics bled rigorously. Master and slave not replaced (yet).

Detailed Problem: The last 5 occasions where drove over 3 hours straight when tried to start the next morning, the clutch was soft for first half of push and would not engage the clutch spring enough making it very tough to get in gear. Got better the hotter the engine got until it shifts perfect. Only happens after long trips when left to sit overnight. Master cylinder fluid level is very much at the top, no leakage anywhere.

Person who did the clutch is experienced but he asked a friend who owns a trans shop with just as much experience and he also was stumped.

If the master / slave are bad, why do they get perfect after getting warm and only are bad after long rides (3-6 hours)? We are talking about 5 instances where this happened on weekend. The next longest ride was 1 hour and the following morning all was good. All daily work commutes have no problem in morning.

Any ideas what to try or look at?

Master and slave are relatively low cost and can cross them off the list. Metal expands and contracts with heat and cold and can effect performance. I replaced both of mine at same time with OEM when having intermittent issues, I forget the cost.
Since you have a fresh trans rebuild and new clutch, and if all bled proper with good lines.....fresh master and slave would be good.

Sent from my SM-N920V using Tapatalk

I paid around $90 for the OEM Master in 2015, I forget what the slave cost. Cheap enough to replace both.

I think the two of them are < $100. Easy swap.

Do it. Just Do It.

Aisin is what is factory for Toyota.
Aisin slave-
https://www.amazon.com/Aisin-CRT-014...ref=mp_s_a_1_3
Aisin master-
https://www.amazon.com/Aisin-CMT-030...KCL&ref=plSrch
I didn't realize it when I bought it, but the master has the port on the side vs the top like the factory master. I just bent my line to go in the side. I briefly searched just now, and I couldn't find the Aisin master with the port on the top on Amazon.
Both cyls for under $70 to your door in 2 days


Edit-
This is the MC with the proper(top) port placement-
https://www.amazon.com/Aisin-CMT-093.../dp/B008EEY2WQ
You can buy the master and slave for under $76.

Thanks for replies. I suppose it could be the master/slave. Also one thing I didn't mention was before the clutch was replaced, the pedal needed to be pushed firmly to the floor to shift at times. The clutch mechanic said the pedal to rod adjuster was maxed out even after his work. I'm thinking maybe it was damaged / pushed forward from a previous accident.

So the followup question I have is: Is it possible the whole problem is due to this adjustment not allowing the rod to fully depress during the bleeding to rid the air from m/s ? Maybe a partial depress of the rod will not bleed the m/s properly?

The mushy feel of the pedal is definitely air in the m/s. Question is, did a faulty m/s allow the air to get in after if was bled properly or was the system unable to be bled properly due to the maxed out pedal adjustment?

Either way, you need a new master. Simple as that.
Have you inspected the master from the inside? My buddy JUST had his master go out, and you could easily tell from the inside that it had been leaking. He had the same thing as you happen in his rig- as far as needing to adjust the rod all the way out, and still barely disengaging the clutch when mashed to the floor.
The clutch system is very simple. Replace both cylinders, document the service, and enjoy.
To bleed mine, I get a clear 1/4"ID hose that's twice the distance between the master and slave in length. Fill the res, put the hose on the bleeder, crack the bleeder, and suck on the hose till it's bubble free. You won't risk getting anything in your mouth, because the hose is twice as long as the systems distance in length. The hose is also larger that the hardline, so it has much more than twice as much volume capacity.
No need for fancy bleeders or pedal pumping.

I got mine from Toyota with port on side. Makes me wonder how much of these "OEM" parts on Amazon and Ebay are counterfeit. I sell my own brand on Amazon and have found counterfeit goods a big problem. The Ebay TB kit I recently got had an Aisin water pump that looked a little odd to me in the stamping and there was another area stamp that looked filled in on the cast mold. Hopefully I'm over analyzing it and its just the way they make them.

My clutch pedal feel had gotten wonky, sometimes engaging low, sometimes feeling soft. I'd had a couple of times where the clutch had smoked instead of grabbing too (off road), and with >200K miles, I just went ahead and replaced the clutch.

Which needed to be done, but once it was all back together, it still felt a bit off. I bled, rebled, no real improvement. Eventually it progressed to occasionally having the pedal stick down, needing to pull it back up with my toe.

At that point I just replaced the master cylinder. And, AFTER ADJUSTING THE PUSH ROD LENGTH!, voila, perfect clutch action and feel is restored.

When I took the old one out I noticed all sort of blackish gunk coming out of it. I think the seals in it had just deteriorated and it wasn't always able to easily pull in fluid from the reservoir. And sometimes it would leak past the piston and back into the reservoir. Whatever, it all works great.

Afte the initial install, it had a whole set of other weird behaviors, they were all related to the rod length not being adjusted correctly. I'm not sure what the proper procedure is, but basically, make sure that the rod retracts slightly from the piston when the pedal is all the way up. The piston needs to be able to return to the very end of its stroke, or it can't pull in new fluid from the reservoir. And if the rod is too short, you'll just put the engagement point closer to the floor.

Well, that just tells me Toyota gave you the wrong part. 3rd gen 4Runners have the MCs with the top port. I bout the side port version too- and it works the same- but it's not the correct replacement.
I'm sure the parts I got were not counterfeit. Not saying they couldn't exist, but I've gotten quite a few Aisin parts in the last couple years, and packaging on everything has been completely consistent. I might be remembering wrong, but I think they all have even had little hologram stickers to show they're a genuine product.

In my haste and sleepy haze I typed side instead of top.
My OEM replacement and original 99, and 2000 parts rig all have top side line port. Maybe some years are different.

Sent from my SM-N920V using Tapatalk

Okay, I was wondering if that was the case! All 3rd gens are top port from the factory

I have had the EXACT same symptoms as OP. Just feels like I have to press way too hard to engage/disengage my clutch. One morning, it did as he described. Let me know if it was your master cyl, as it does sound like it. Thanks!