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I recently purchased a 99 Honda civic dx manual transmission. When I bought the car it had a slight grinding(right word maybe?) noise when idling. When I pushed the clutch in the noise would go away so I thought it might be a throwing bearing. After dropping the trans, replacing the part, and putting it all back together and performing a tranny flush, it will now not shift into fifth gear(reverse is iffy as well) nor did it fix the noise. The clutch is good and it drove great into all gears before I disassembled anything just had the noise. I don't think the little noise has anything to do with it not going into fifth, maybe a pilot bearing I'm not sure. Would it be the shift linkage may have slightly bent? Dont think its the fifth/reverse shaft in the trans because it worked fine before. Could it be because I didn't specifically use Honda manual trans fluid? And while I'm at it what could this noise possibly be at idle without the clutch pushed in? Any help would be greatly appreciated as this has been a big headache. Thanks!

 
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your thread is posted on the 2012 civic section...
99 is 6th generation...

 
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Whoops, sorry never used the forums. I'll repost