I guess we are on in the same boat. My 3rd gear syncro was acting up too. I pulled the transmission apart and there were a lot of things wrong with it, bearings, and crap. It would have took over $700 in parts to fix everything including updating the 5th gear, so I ran over to Ft. Worth to Standard this past Sat. and picked up a fresh rebuilt one with the fully splined mainshaft already done.
The part # on the rear main seal is 4089342 I believe... . that is what was for my '94.
I also worked on stabbing in the 13" FE and transmission in last night, but didn't have any success. I know what to do now, got to start all over.
Some advice, on the 13" clutch, take the starter out first before you put the flywheel on. Then put the starter back on with the Aluminum spacer and longer bolts. I almost messed up. :-laf Also, its a good idea to put a dab of thread locker on the flywheel bolts, they'll still come back off with an impact if it ever needs to be pulled back off.
Oh, and this is what I got to redo, but make sure when you put the clutch disk in with the plastic alignment tool that comes with the kit, make sure when you put the clutch basket on and start tightening them down to check and see if the alignment tool will come out easy still, if so keep snugging everything up... . then tighten at 20-25# lbs. and pull the tool out. I'll be doing that over tonight.
Just some advice I wish I would have known myself before attempting.
Later,
Justin