You get in a situation like this and it's hard to tell exactly where the fault is. Possibly a wire pinched either in the accident or during repairs? Yes the AAM controls interior lighting AND the runnin boards, sorry I don't have any specific circuit info.
Is the bodyshop one that was recommended to you by the dealer? I would always ask the dealer who they recommend.
At this point, assuming repairs are completed and the B/S
has been paid, I'd say you need to contact your insurance company and tell them that you are dissatisied with the repairs on the truck and you need to take it back to the dealer to get things squared away.
Gilly