Basically, I had to assembly everything using plane and axis connections, using extra connections after the part was fully constrained (setting different planes rigidly to the motion skeleton parts). Then, the assmebly as a whole was attached in the same manor to the correct planes in the high level skeleton, and boom. It works, and well might I add.
I altered a bit and used your mechanism link check for the ball bearings as well. It was all done primarily through motion skeletons, though, so that it is more adept to fitting into a top down design methodology (mechanism links positively will not operate top down, so there is some user alterations, but not nearly to the level that I imagined there would be).
On a separate note, do you know of any references on tandem part creation? For example, creating the helical sweep of a worm drive and the gear to go with it.