I finally got around to remembering to bring in my paper from the dealer. Here is the official list of parts replaced, with part numbers and quantities:
Qty Part # Description
1 BR3Z-7048-A Input shaft seal
1 BR3Z-7A010-A Blanking plug
1 CR3Z-7017-A Input shaft
1 CR3Z-7144-A 5th speed cluster gear
1 BR3Z-6375-D Flywheel assembly
1 BR3Z-7B546-AE Clutch assembly
9 W715869-S439 Self-locking bolt and washer assembly
6 W715869-S439 Self-locking bolt and washer assembly
2 BR3Z-5B266-A Gasket
4 BR3Z-5A231-C Clamp
1 TA-26 Adhesive
1 TA-30 Silicone sealant
3 XT-11-QDC Transmission fluid
1 BR3A-7124-DB Synchronizer hub
8 BR3Z-6379-A Hex head bolt
1 PM-1-C Brake fluid
3 N800594-S100 Bolt
That's everything on the work order I received. The technician comments are this:
VERIFIED CUST CONCERN CLUNK WHEN RUNNING STILL WHINE IN 1 THROUGH 4TH GEAR GOES AWAY IN 5TH AND 6TH REMOVED TRANS INSPECTED PRESSURE PLATE FOUND HALF OF THE RELEASE SPRINGS FURTHER RELEASED THAN OTHERS TORE DOWN TRANS FOUND INPUT SHAFT AND COUNTERSHAFT FORWARD GEAR TO HAVE EXCESSIVE WEAR GEAR CLASH CAUSING WHINE REPLACED WITH NEW AND INSTALLED NEW FLYWHEEL CLUTCH DISC AND PRESSURE PLATE FILLED WITH NEW DOUBE DRY CLUTCH ATF VERIFIED REPAIR
This has completely eliminated all gripes I have with the transmission itself. I do still have an issue with the shifter being too far forward in the console but after taking it back once to squak about that I won't take it in again as I want to maintain a good relationship with them in case I need them in the future. So I'll bite the $130 for a new shifter assembly from Tousley and replace it myself.