Doesn't sound right to me that it would be OK and then lose reserve and then get better when bled again, but only sometimes. It jest haint natchrul.
Shimming the flywheel? Do they mean shimming the clutch cover away from the flywheel?
Sounds hokey tummy.
Do you know if when the clutch was replaced that the trans input shaft was checked for rust on the splines? If it was rusty, they should have taken a wire brush to clean it up. Also, they splines need to have a thin coating of lubricant (grease) to protect them from rusting, which will definately lead to the clutch disk sticking in position and not moving away from the flywheel when the release bearing pushes on the clutch cover spring and the pressure plate moves back away from the flywheel. This would tend to act like a clutch that drags all the time - it shifts nice when the engine is off, but with the engine running you might not be able to get it into Reverse and all the other gears require high effort to shift into as well.
I think shimming the flywheel makes sense if it is turned thereby changing the surface the clutch cover attaches to, so as to maintain the same distance between the slave and the clutch fingers. Shimming the clutch cover would be simpler and is an interesting idea--not sure it would work. Also thought of shimming the slave.
But your thought on the rusty splines makes the most sense. Rusty splines would explain why under load it releases much higher up the pedal than when trying to get into gear at idle, because under load the high load with rpms breaking it free would tend to separate the disk from the flywheel or at least over come any resistance. At idle that would not happen. But then why was there good pedal after the hydraulics were installed and on the first bleed?
Now it is 1/4 or so of reserve but when I take off (and this was true after I lost pedal before) it feels like it is grabbing weakly but enough to hinder getting into gear from a stop. The real grab still seems to be an inch or more up the pedal. I had been thinking warped clutch disk as that would keep spinning when released, but your idea makes much more sense. Whelp, maybe we pull the tranny. I have to ask him when he had it out for the slave install if he looked at the splines or put any lube. I wonder if there is a lube spray with a very long plastic tube I could get up in there through the inspection hole and give it a little squirt, maybe silicon, then see if it works better.
One other thing there seems to be a slight roughness when I work the clutch with it running such as if the release bearing or clutch disk were not sliding freely, but that is very subjective to feel and may be just some other part of the system.