There is a knocking sound coming from the transmission while the car is running and in neutral.
I just finished reinstalling the transmission and a new clutch.
I ordered the Exedy "MazdaSpeed" clutch from BHR a while back and followed Charles's directions to shim the pressure plate.

"Use a set of six (6) copper washers in the .060"-.080" thickness range and install them between the flywheel and the pressure plate. This will improve the feel and the action of the clutch."

I had some washers in the shop that were withing this range. I measured them with a caliper, ran them across some sandpaper and measured again. All 6 washers were at .070".

It sounds to me like the pressure plate it rubbing up against the bellhousing somewhere.
I'm not sure how much room was in between the pressure plate and the bellhousing to begin with, but could the added washers be the problem?

 

erratic knocking or is it consistent?
how many miles are on the transmission?
did you drain and refill the transmission with new fluid and if so was it factory spec lubricant?

sounds like either a tired transmission with lower viscosity oil that is exaggerating the gear backlash or the pressure plate is just too large and is rubbing on something in the bellhousing.

 

Consistent knocking that speeds up and slows down with engine rpm.
It is a used transmission with about 45k miles on it.
New clutch, pressure plate, and t/o bearing. The transmission was refilled with Redline MT-90.

 

try pulling out the starter and see if you spot any metal shavings in the bellhousing.

 

Well, it looks like I'm just going to drop the tranny again. I've got some MT-90 coming from the bell housing, I guess I'll be replacing my input shaft seal again also.

Thanks for the insight though.