my 2000 civic ex has had a bad pilot bearing or throwout bearing for the last few months. it clicks when in neutral at an idle with your foot off the clutch, and also clicks faster with the rpms as you excel through 1st 2nd and 3rd gears. so today i put in a clutch kit, bearings pressure plate and pad.... still clicks... could my trans fluid just be low and what kind of fluid goes in there?

the mission was not a total failure though, i also added lowering springs (-2.5") and replaced a leaky rear main seal while i was in there.

 

it could be your input shaft bearing if it increases with engine speed. before you get worried, open up the fill plug (it's the one with a fitting for a ratchet) and fill with either honda manual trans fluid from your local dealer, or 10-40 engine oil. with the car at ride hight, fill right to the level of the plug, dont try to jack up the car thinking if you tilt it you can get more in there. more isn't better in this case.
a bad throwout bearing would only make noise when you step on the clutch. a bad pilot bearing would only make noise when the clutch is depressed (so the flywheel and input shaft can turn at different speeds.) a trans rebuild is expensive labor wise, try the fill and see if that helps any.
however if it makes noise in all gears except fourth, then it could be the pocket bearing that connects the input shaft to the output shaft. in fourth it wouldn't make noise because fourth is essentially direct drive, meaning both shafts would spin at the same speed (or VERY close to) so the bearing wouldn't be turning (as fast.)

 

alright, that all makes sence, i think the reason it does not click in 4th or 5th is because i rarely run those gears all the way out, i don't hit the high way much. it really only clicks from like 3500 or 4000 to 7000, and also wines while down shifting to slow the car.

 

It's pretty simple to just replace a few bearings in the transmisison, you probably don't need a full rebuild.

It's also a lot cheaper in the long run to use the brakes than to routinely downshift.