Noisy tranny (?) very disturbing - please help with some opinions or suggestions
 

1999 model with approx 98k on engine and aftermarket clutch about 3k. Started making a chatter/rattle noise very suddenly after approx a 40 mile drive and a brief stop. Noise present in neutral as well as while driving. Sounds horribly worst in second gear. Cant say if present in 4th or 5th as maybe road noise drowns it out. Sound goes away when clutch pedal pushed to floor. Driving seems normal with exception of the noise but I haven't driven many miles since noise first appeared. When i did drive, in particular when i had to drive the 40 miles back, i shifted 1st to 3rd.

Any suggestions on where i should start? Tranny? Clutch? Crank Thrust bearing? Would like to rule some out before i chase down a shop. My clutch guy didn't even listen to it or drive and immediately said tranny. He may be right but he may also be trying to avoid some liability on his recent work. Can i rule out the thrust bearing issue that some 99's have faced?

Thanks in advance .

It is the throwout bearing. Your symptoms are classic.

Always put a new one in when you change the clutch, and always use a non-chinese bearing.