I don't know much about electronics but if you didn't let the smoke out, I'd think it is probably not damaged much.
It is hard to believe the runaround you are getting.
Since this problem started with battery work, have you rechecked all the cables and wires and ensured they are connected/grounded correctly?
Is/was there a fusible link somewhere upstream of the transmission.
I have all the batteries are correct now, I have full voltage to all the trans controls, I don't know if there is a fusible link, I have looked and cant seem to see any. Prevost only used this transmission 2 years and it is the first year for Allison to use a electronically controlled unit. Nobody knows much about it.