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I did check the pedal and the linkage when I rebuilt the master, but I'll check again. I know for a fact that the shop didn't replace the bearing (is the pilot also called the throwout bearing sometimes?). I just assumed that it was done when a new clutch was put in so I didn't ask until after (my own fault). Guess there's no way to know for sure without having it all taken apart again huh?

Pilot and throw-out are not the same. Both bearings should always be replaced when the clutch is done, especially the throw-out.
Before going to the expense of the clutch itself, replace the MC with a new one (they are inexpensive). Most people don't rebuild those things anymore. A bad MC can also cause those symptoms.

Rick
1984 4Runner