I have a 93 4Runner with an automatic transmission. The coolant line broke, trashing my whole transmission so I had to get it replaced, and they replaced the whole thing (including soleniods), and it is still under warranty.
I drove it for a few months after it was fixed and it was fine, then noticed it seemed to be revving high when it shifted into 2nd gear. This kept getting worse, until finally it would go over 3000rpm's before shifting, the go into 2nd and third at almost the same time.

I took it back into the shop that did the transmission, and they replaced the clutch, but that didn't fix the problem.
Next they replaced the speed sensor and kickdown cable. They test drove it and said it was fixed.

I picked it up and it wasn't.

But I did notice that if it is cool, it works great. (Which is why they thought it was fixed. They only did a 5-10 minute test drive) After driving for 20 minutes or so, it starts to act up. Anything over 20 minutes and it is nearly undriveable. It was revving all the way up into the 4500rpm range before shifting into 2nd.

All the other gears seem fine.

Any ideas based on these symptoms? They have no idea.