This is a really interesting post. Clutches are great as long as they work and are easy to replace as long as all goes as it should. BUT if a component goes south, they can be a real PITA. In my son's Miata he had intermittant clutch issues, not disengaging, same as OP. Replaced slave, replaced master (hydraulic clutch), checked PP, CD and TOB, but every couple of months the problem seemed to return. Finally traced it all to a softened section of flex hose between the master cylinder and the clutch slave. It woudl expand and not allow the hydraulic pressure to fully disengage the clutch.
Long story just to say, part of the issue might have been a clutch cable reaching the end of its life and stretching each time the clutch was engaged. This is extraordinarliy common in Volkswagen beetles (cable operated clutch) and motorcycles. I know all to well from experience.
Before you put it all back togehter you might want to check out the input shaft bearing in the transmission. Operating without a pilot bearing for extended periods can damage that front bearing in the transmission.
Good luck and keep posting, you have lots of support and I applaud you for not getting overly frustrated with a seemingly simple fix. If is was me, by now, it might have felt the heat of the cutting torch.