Jim, could you explain how getting rid of Clerics works in your games? When you fold the Cleric spell list into the MU one, did you just combine the lists level for level and then roll on a larger random table? Or did you get rid of some spells to shrink the options? Do you move spell levels around since Cleric spells have 7 and MU 9?
More generally is there a series of posts that goes through your thought process on the current rules and explains why you picked the spells you did and the particular versions of the mechanics you use? I'd like to understand your thought process better b/c it would help with making ruling and adopting house rules. (Maybe when you make the next edition of the Referee book you can get into this.)
Re: the changes you proposed, I think the best way to do this while keeping everything clean is to have multi-classing as the norm but with each class doing only one "thing" when you take a level: fighters give you bonuses to hit, magic users give you spell slots, specialists give you skills, someone gives you better saves (or have each save be its own thing), another one gives you better HP, etc. Conceptually, all the "extra" classes that other systems have are just various combinations of these basic mechanics. And making it explicit would improve on the keep the clean separation that your system has while still allowing for the more elaborate variations you are interested in having. Doing it this way would would make the criterion for a new class quite clear: a class alters some one thing on the char sheet.
You could put "recommended party roles" into an appendix and give the progression for each type of character you use in your own campaigns with the optional rule that the roles were mandatory. And as your usage of the game evolves (or as different GMs apply different house-rules), roles could change without altering the underlying mechanics of the game.
The one area where this is problematic is that magic users get research abilities and fighters get combat maneuvers. So you'd either have to let everyone do them or you'd have to have a dual system with classes adjusting your stats and roles giving you access to certain mechanics.
Personally I'm in favor of the first option (if you've taken a level in fighter or in MU, you can do those things). That keeps the system clean and it doesn't result in a pull for unique mechanics for each role. If you start creating unique mechanics for everyone, you end up with Pathfinder. Admittedly it sells books since players have to buy guides to use the cool new toys, but I think it ends up cluttering the system unnecessarily. And in reality there probably aren't many class features that can't be mechanically accounted for by designing an appropriate selection of spells for a role-specific spell-list.
Edit: So, I took a look at the playtest document thing and got answers to my questions of how the changes worked. I'm not sure how relevant my suggestions are in light of everything you are changing. But you are free to use the ideas if you want.