Ben,
Yeah, I think the electronics are OK. Anything/everything I've checked seems to be normal and nothing about electronics explains the strange behavior I'm seeing.
Everything that I can get at without pulling the table seems just fine. Pulleys, belts, X-axis screw turns freely. I can't turn Y manually as there is nothing to to turn.
Unless or until I can get someone to help I'm pretty well stopped out on this. I can't get the table off unassisted and the X Motor will have to be removed to get the table off the end of the screw and the rails due to the enclosure.
I have often wondered about the long time frames of the CNC projects that people talk about on the forum and now I'm beginning to see why nothing gets done quickly. ;-(
I'm not sure exactly what you mean "by hand"?