I had similar issues with my car which had it's body work finished, painted, glass and driveline installed at a well known Midwest restoration shop. Front fender was misaligned, I was very fortunate to know a local body shop and E body owner who came to my house and fixed that for me. When I told the restoration shop owner my progress on reassembling the car was delayed by that and side glass alignment issues, he said I have drilled a new hole and relocated the hood pin so it fit correctly in the hole in the hood rather than realigning the fender to be correct. (ya can't make this sheet up....)
With the glass, they didn't even clean up or lube the tracks before installing. My body man friend and another buddy helped out fixing that. The restoration guys response? The glass was aligned when it left my shop. Seriously??
I don't have complaints about electrical. I installed new M&H harnesses myself other than the dash harness I had a local Mopar guy who does electrical and gauge restoration as a side business go through for me. I'm an idiot when it comes to electrical. In college getting my mechanical engineering degree I got Cs in every Electrical engineering class I was required to take. I was careful to make sure I had good grounds and used dielectric grease on many connections, and after working out a few bugs, all my electrical is working fine. If an electrical moron like me can do it, it isn't very difficult, so no excuse for a professional shop to send out cars they've restored with electrical gremlins!
I hear more bad stories than good about restoration shops, it seems par for the course. I theorize fumes from paints and chemicals in shops affects these guys brains and turns them into flakes!