I have not encountered it before, but driving a car with a 20G without a tune is not wise. I know the standard "keep it out of boost" that people go by, but driving with out a tune cannot help. I would suggest you get at least a base tune from a tuner to get to the tuner and see what happens with the trans. As far as how it effected the transmission well that is weird. Its tough for them to tune the car if the tranny is not working.
Search for tranny codes. There is a way to read the codes from the flashing light and it might give you more information about what might be wrong. Could be something electrical, you never know.