NEED HELP.I GOT A 95 EX 5 SPEED CIVIC .NOTHINGS STOCK INSIDE OR OUT. BESIDES THE ENGINE. N THE TRANNY.THISE IS MY 2ND CIVIC.AND IVE NOW HAD THE SAME PROBLOM WITH BOTH .WHEN IM IN NEUTRAL IN MY GEARS IF I PUT THE CLUCH IN I CAN HEAR SOMTHING LIKE A BERING IN THE TRANS SPINNING TO A STOP. THEN IF I LET THE CLUCH BACK OUT AGAIN I CAN HEAR IT START SPINNING AGAIN .ITS STILL VERRY DRIVEABLE. BUT ANOYING . AT THE SAME TIME. BUT SOMETIMES. IF I GET ON IT AT HIGHER RPMS . THEN I SEEM TO MISS SHIFT N GRIND THE GEARS. IT JUST SEEMS WRONG IN THEIR?. MY LAST CIVIC WAS A 93 DX . AND IT DID THE EXACT SAME THING . I TOOK IT IN TO A TRANNY SHOP N THEY TOLD ME THAT IT WAS A THROW OUT BERING .MAKING THE NOISE. THE CIVIC I GOT NOW THE 95. ITS THE 2ND TRANS IVE PUT IN IT AND BOTH OF THEM DO N DID THE SAME NOISE. NOTE BOTH TRANNYS WHERE USED... CAN ANYWONE TELL ME WHATS UP ???????????? THANKS CRAZZY J

 

I have the same thing with mine I think its the throw out bearing but It could be the input shaft bearing both are cheap fixes but time consuming.

 

A throwout or release bearing will make noise when the pedal is pressed, when the pedal is out it's quiet. You can drive itthat way for awhile but eventually you'll have to replace it before it grenades. While you're in there do the clutch too. It's a labor intensive job & you don't want to do it twice.
xmctech

 

it sounds like you are replacing transmission when you just need to replace the part that is defective.
i am leary of trans and motors from junk yards (dont know if that is where you got them, though).