If you need to train the companions you want to be vassals, and not in your party, you could just send your normal companions on missions or tell them you need to separate for a while as you train the others.
Also, since its just a means to an end... you could just cheat a little bit to move the process along, since its so bugged / incomplete.
But some people don't like cheating at all. If that's the case, you have a long, boring road ahead of you, until some decent mods come out :-/