Well, I would replace that missing ball first. If that doesn't help, then I'd tear into the clutch again and check the spacer washer positions. But, before tearing it down, with the right cover off, I would pull the hand lever and observe the clutch pack to see if the plates are moving, if the pressure plate moves out allowing the other plates to release.
You said you obviously had to replace your clutch because it sat for 5 years. I'm not sure why you thought that. I still have the original 35+ year old plates in mine and they work just fine. Most I've run across work just fine unless they're worn too thin. That's about the only reason I would replace any. But, something else has occurred to me. How many friction clutch plates did you put in? The clutch pack design changed around 1980. The new design uses one less friction plate than the earlier unit (6 instead of 7). If you crammed 7 friction plates in your later unit, that could explain why it won't release.