I got an answer from George at Netgain, as to what that stuff was that was laying in the bottom of the motor. Apparently all that debris is balancing putty. Well, that explains everything nicely! It totally makes sense now. Why the motor and clutch were balanced at first. Why it seemed to fall out of balance all at once.
Without a moments hesitation, Netgain has told me to prepare the motor for shipment, they're sending someone to pick it up to take it back for repairs. Now that's customer service!
It's sad to see it go, but I'm thrilled at the prospect of getting it back balanced, strong and ready to go back in the car.
Now onto some other improvements on the car while I await the return of the motor.