Dave,
I'm back with a couple of links you might not have found:
Endless-sphere.com • View topic - e-Buggy: Alternator Conversion
Endless-sphere.com • View topic - Adding hall sensors to outrunners
Analysis of a REEM inadvertently used in a reverse power flow condition. - RC Groups
I have not put anything on paper or a breadboard yet but I'm planning on making the controller modular with mcu, optoisolator, driver and power boards.
This should make troubleshooting easier. Lots of little hairballs instead of one big one.
Chuck