I just did the auto to manual swap on my 00 civic ex and put in a 96 hydro manual trans with new exedy stage1 clutch , act streelite flywheel , TOB and pilot bearing and filled with honda mtf. Ths trans is making a grinding noise at idle and speeds up when you give it gas while in gear but goes away when you engage the clutch and comes right back when you disengage it. All gears hold fine except for 2nd gear which will pop right back out as soon as you let the clutch out and grinds like crazy. I have read so many pages on this here Im not sure what to try besides replacing the trans .

Any input in this would be great as the car is running fine and rest of the swap related stuff went perfect no codes or anything

 

You got one or more bad bearings inside the transmission and the 1st-2nd synchro set and 2nd gear should be replaced.

It'll probably cost about $400 to $500 worth of parts.

 

sounds like I bought a real winner