After consult with the internet and smart Corvair folks, It would seem that the only solution to these rubbing issues would be to raise the motor up a bit in the rear. Using some square metal tubing, I added about 1.5" of height to the rear motor mount.
Unfortunately, raising the motor means I need to find a new home for three of the 44 batteries required to power the car. They are too tall for the space they once occupied. However, this does open up some space for a DC-DC converter.
Still, running on just 41 batteries, I was able to drive the car around a bit and all the rubbing issues are gone. The drive axles are now sitting at an appropriate angle within the a-arms.