And now to add to my frustrations, something part of the clutch system inside the bellhousing has decided it no longer wants to work correctly as I can no longer get the car into gear with the engine running. I found that the master cylinder was leaking around the boot at the firewall, so I took it out and rebuilt it, and fully bled the system until no more air came out, then I did an additional gravity bleed just to be doubly sure there was no air. No dice. Readjusted the master cylinder rod to ensure maximum piston travel in the master cylinder. Still no dice. Check the slave cylinder throw, definitely throwing more than far enough for it to work correctly, and it was not leaking any fluid. Tried rocking the car back and forth with the clutch pedal in and starting it in gear with the clutch pedal pushed in just to see if it was the clutch disc being stuck to the flywheel, still no dice. This leads me to believe it's likely going to be something fun like a bent clutch fork, or a flogged pivot ball clip, or broken pressure plate fingers, or something along those lines, all of which require pulling the transmission off to fix. (and there was much rejoicing).
So, in order to prevent me from having to pull the box off again in the near future, I'm going to take the opportunity to do as much work as I can afford to in one go. Forged clutch fork, new pivot ball, new clutch, new throwout bearing, and some kind of center diff upgrade, as that's much easier to do with the box out than box in. If anyone has any leads on someone selling either a Cusco Tarmac Gear center diff for an CD9A/CE9A (long shot, I know), or a 4-spider converted stock center diff, I would much appreciate the heads up.