Hal, what you describe does sound like issues in the hydraulics. There's not that much to the system, so I'd give the whole thing a 'once over', um again I suppose. Use the FSM as you go. Inspect the hydraulics, tighten all nuts, bolts, flanges and fittings, etc. then bleed the clutch properly once more. You may have a bent fork. It might be possible for you to peek into the whole where the fork is and see if that is the case or not. You might even see if it wiggles in strange ways. That would be a sign that maybe it's off the pivot ball or off of the throw out bearing carrier. Try and peek into the bellhousing. A bent or dislodged fork will limit the movement and not allow full clutch disengagement. You may have the incorrect Master cylinder. I bought a new one online for my 240 and the input shaft was much shorter than stock, so the pedal never got full travel and it didn't work. I had to throw away that master cylinder. You may have the incorrect slave cylinder. If the piston on that isn't long enough to push your fork all the way, you won't get full clutch disengagement.
If your clutch worked properly for a while and now isn't working properly, then you probably don't have to worry about the parts being the wrong length. If they were wrong parts, you'd have this problem the whole time since installation.
Your experience with normal clutch wear is typical and I agree with your assessment.
Here's the the best I've got for a Service Manual: http://www.nicoclub.com/service-manual? ... e%20Manual