I replaced the clutch on my '88 4Runner (5 speed manual, 22RE, 320,000 miles) about 50,000 miles ago. I'd never done a clutch on a car before and found at the time I couldn't remove the pilot bearing so I left the existing one in place (this was 3rd clutch, other 2 done by Toyota factory/dealer, respectively). After I finished the 4Runner has run fine; however, about 20,000 miles ago it developed a rattle which I think may be the pilot bearing????
The rattle is present in 1st, 2nd, 3rd and 5th gear, and at idle, but not when in 4th gear. When I'm sitting at a stop in neutral if I depress the clutch pedal the rattle goes away (not instantaneously, but very quickly--like something slowing to a stop) and when I let the clutch pedal out it comes back instantly.
The only thing that bothers me about attributing it to the pilot bearing is the absence of a rattle in 4th gear.
Any thoughts would be appreciated?

 

That is strange. Although I don't know what advice to give on the rattle I do know you can remove the pilot bearing with wet news paper and a bolt that fits in the hole, that's how I pulled mine.