I just had my engine rebuilt (improved), added a SPEC stage 2 clutch, aluminum flywheel, 383 stroker, porting, etc. I had 157K mi on the original engine, transmission and clutch. The clutch was going, but still ok. No strange noises.
Now when the car is in neutral, and idling, I hear a kind of quiet grinding or rattling(sort of). When I depress the clutch, the noise goes away. When driving the noise returns when coasting. Under acceleration or deceleration, the noise goes away. It could be synchros or bearings? Any ideas or suggestions? Thanks.

 

Bad pilot bearing possibly, was that replaced when you installed the new clutch? Even if it was replaced the new one could have been damaged when you installed the new clutch, especially if you had trouble getting the trans to slide in and had to force it in at all.

 

I have the same rattle. Wasn't noticable with a stock cam but once I swapped in a lumpy one it started rattling like crazy. It only rattles when the clutch is out and in neutral. Turned out to be the heavy shift fork that was/still is rattling away. Five seasons with no problems other than the annoyance factor. Sounds exactly like what i have.