A lot of keyboard sheetmetal guys put AMD wayyyy up on a pedestal and call them plug and play panels, but obviously from your posts and feedback from us other guys about AMD, their perfection panels do not exist. Now compared to some other manufactures, they do have the best fit, but again, obviously not perfect. I've heard that the Charger panels gave folks headaches from time to time Hunt2elk. Especially if they've been running the tooling for quite a while. I too had conversations with AMD about panel issues on my RR. One of the issues they admitted to having complaints, the others said they had no negative feedback, which was pretty unbelievable.
Myself I would send AMD a pic of that crap fitment with the deck filler, tell them to send you another to see if it fits better and if it doesn't...well, use it to graft out a slice to extend the other. Either that or graft in your own cut/shaped metal. Lot of extra work....almost be worth looking for a donor, but that would be like trying to find Atlantis. I'm sure you could massage the quarter/deck filler to get a little closer, but my guess is in the end you're still gonna end up with a bit of an irregular gap.
As far as your tail light issue..I'd be pretty ticked as well. That is a lot of extra work. Pay that much money, a guy would figure they'd be right, but not so much. All part of the fun I guess.