Hi Bob,
Clearly you know electronics so that is a plus. I'm hesitant to give any advice seeing as this is all off of memory for me. Fundamentally I think you have a valid point, however, if they putting the legs into a full wave rectifier. Clearly their goal is to get DC and DC obviously has no phase associated with it! Sounds kind of strange to me for a brush type amplifier to use three legs in the amp. My conversion was easier. They simply had a single phase transformer, etc, etc. So all I had to do was get each of the different single phase pickoffs all going to the appropriate 220V lines and bingo! I had a machine that was running 220V single phase. As I said, the only tricky part was the GE 3-phase spindle motor, but I just derated a 4HP VFD for that. It all works like a champ now.
I'd hate to give you much more in the way of suggestions on your machine without really being able to look at it with schematics in hand. Sorry.
As for your other question about Mach1. Unfortunately I have no experience with it. I guess my feeling, however, is to use what you've got for awhile until it either breaks or is deficient in some fashion. I have no real need for 3D contouring, so I don't see the push to convert for such functionality.
Alan