I rebuilt my motor about 5 thousand miles ago in my 1st gen 4runner. It's got the 22re 5 sp. When I pulled the motor, I also put in a new clutch kit. 2 weeks ago my clutch started to make a weird noise, so I pulled the tranny. My throwout bearing (only 5 thousand miles on it) was wore down close to the clips. The clutch disk, pressure plate and flywheel all looked good, but i replaced them all anyways. I got it all back together and it is driving and shifting fine.

Here's the problem. My clutch pedal engages at the top, and i think is why the throwout bearing wore so fast. I tried adjusting it by pulling the pin on the pedal and tweaking the push pin that goes into the master cylinder. This did not do any noticeable difference. I checked the slave cylinder (which I replaced not long before the motor) and it was right up against the fork even though not engaged. I took it to a tranny shop and the guy told me to cut the pin that is attached on the pedal in order for it to engage later. I think the guy is full of crap and there has got to be a better way. Anyone experienced this and know a possible solution? Thank you

I haven't had to deal with this on a Runner yet, so I'm not sure if this applies--is the actuator rod in the slave cylinder threaded, to where you could screw it in or out to change the engagement point? My current one is aftermarket (it's a larger Landcruiser unit), and the fork end is threaded, with locking nuts that I can move back and forth as needed. Just thinking out loud.

You should not have to butcher a part to get it to work correctly.
You need to find out what is really wrong and correct it.
My first thought is it's an installation problem.
Are you sure the TO bearing and fork are installed correctly?

It is not threaded and can not be adjusted. Mine is after market too. Thinking I will buy a new one and see if that is my problem.

TO bearing was installed properly. Checked before I took it off. I took off the fork when I replaced the TO bearing and made sure it was on correctly. So I am pretty sure neither are the problem.

you need to shorten the MC pushrod.

for whatever reason, i have ran into a couple that were too long, and when adjusted as short as they would go, before hitting the pin, it still wasnt in the right spot.
and we had to cut 1/4" or so off the threaded end.
make sure this is what you need BEFORE you cut it.
and also, try this before you buy another one.