Final update: I got the car back and im not paying a dime. Avalon is giving me a refund on the tune and replaced the ECM and did all the labor at no charge. As of right now the car is going back to stock and will stay that way for awhile.
As to what caused the failure is still unknown to me but to be honest, I dont care. It got handled professionally and it didn't cost me anything but a little bit of time.