The solution, if anyone else runs into this:
I finally got around to pulling the transaxle again, and found the problem. The clutch diaphragm spring was bent slightly (about 1/16" shorter than the new Exedy one). The clutch disc was just about flush with the rivets (as far as I know, it had 123,331 miles on it). The flywheel had 3 heat marks evenly spaced around the friction surface, I didn't measure them, but they seemed to make a nearly perfect equilateral triangle, the friction surface had a slight ridge where the clutch disc contacted it. So all in all, I'd say there was probably about 1/8" to 3/16" of wear that was allowing the slave cylinder to overextend. I replaced the flywheel, clutch disc, clutch cover, and slave cylinder. It drives like a new car, takes much less effort to change gears. It never seemed excessive, but now it just falls into every gear. I think the clutch diaphragm spring being bent was causing the clutch to not fully disengage.