I took the flywheel/clutch to Dan Halls Machine Shop this morning and just picked it up half an hour ago. Dan basically said that it was fine. He spun it as fast as the machine would go and it was only out of balance by 2 grams on the flywheel and 2 grams on the clutch pressure plate. Apparently this really isn't a lot for flywheels.
The motor adapter hub from Electro Auto still has 4 mils (thousands of an inch) runout, so I'll try to attack that next. Dan suggested that I try attaching the hub without the shaft key to see if the runout goes away. That way, I can see if I need to modify the inner cone or just the shaft key or its slot.
On a brighter note, I got an e-mail from Beth at Azure Dynamics mentioning that there was an RPM output on the DMOC445 controller that I might be able to tap into and drive the RPM gauge with (given some external converter circuit). There's also an SOC (state-of-charge) output and amp-hour counter inputs that I might be able to try out as well. There's no documentation on these pins, of course, but I'm happy that they're there to try out.
Next Up: fixing the tiny (4mil) runout on the adapter hub...