Just got back from round 2.
Better fit then before but still no "off the lot" look.
The knife they used to break the seal and get the glass out cut a huge gash in my paint as well, which they put touch up paint on. fawk that.
They offered to fix that with some other guy that can come in and paint match but I decided to cut my lose at that point, said thanks, drove down to the Jeep dealer main body shop and setup a date to get a quote for fixing the knife gashes (paint whole rear panel I guess) and re install brand new rear quarter glass.
These are the guys who fawked the Jeep up. Which was recommended from a well known body shop, guess they had the C Team on my Jeep both times I went...
A few brand new challengers and even one srt8 parked out in the employee lot at the dealer body shop, so job quality should not be an issue, should have gone this route the first time... will keep you posted.