I seem to be having a very similar problem as Kevin A has... it became difficult to shift, so I assumed the cylinders and changed both master and slave, as well as the rubber portion of the hydraulic line.
At first I had Centric cylinders that were available locally, but despite bleeding multiple times, and multiple methods - all mentioned above, I still had trouble shifting into first, 5th, and reverse. I got AISIN cylinders from Amazon, but didn't improve. This been going on for almost 2 months, and right now I have the Centric master and Aisin slave, but shifting is still often difficult.

What else do I check? How do I remove the fork to check it?
Are there synchro gears in the transmission that might cause this? I assume that would require a complete rebuild??

thanks

 

From the Info I have found here, I began chasing the problem like this.

Is the clutch bracket okay? Several have been cracked.

Is the shifter bushing okay? Located directly under the shift lever, do a search and there are good instruction on how to replace and it's easy.

You have repaced all hydraulic components, it sounds like, that's what I did.

The fork can be found in the trans bellhousing, the transmission must be removed to replace it, good time to do the clutch and resurface the flywheel if you are due for a clutch anyway.

I have not received my parts to go back together yet, but will let everyone know how it works when completed.

Yes, I am a little worried about the synchros too, we'll see when I get it all zipped up.

 

I thought I would give an update on my Yota.
I replaced the clutch fork and when I got to looking, the throwout bearing was completely shot! I mean shot as in the "prongs" of the fork were pushing THRU where there was once two flat spots for the fork to push on !!

NO WONDER the dang thing would not shift right !! SO, I now have a new master Cylinder, slave cylinder, clutch, throwout bearing, fork, pilot bearing.... I wish now I would have replaced the little "ball" the fork pivots on but oh well....

It shifts and clutches like a new one !!! It has never worked this smoothly, (not even since I bought it!!) and now I think the guy traded it to avoid this trouble ! His mistake because after a few hundred dollars, it is working perfectly !!! Remember I said that the clutch was like a bear trap and my leg would almost get tired in city traffic? No More !!! It works great.

I am amazed that we were able to wheel for days on end in the San Juans last summer with the way everything looked inside !!! I am sooooo glad I made it home from that trip.

THANKS TO EVERYBODY that gave me tips along the way, it gave me the confidence to tear into it and get it going !!!!!

 

KevinA, Thanks for the update. Dead End Threads Suck.

Glad you got it going and get to enjoy your truck.