Issues with them mounting the Kelderman air ride, I had to redo several things as well as finish a few. Issues with them scratching it numerous places, a detail shop was able to buff out most of it, but one window will have to be replaced and my local body shop is working up a bid to repair the scratches on the bed and tailgate that went completely through the paint. Honestly, for them being a body shop I'm VERY disappointed in the condition I received the truck. It literally looked like a 10yr old washed it in the driveway when I picked it up. Mark was actually pretty embarrassed. For what is now a $95,000 truck with less than 1,000 miles on it, I expected them to take a little better care of it. And lastly, they blew up my stereo (and I'm hoping nothing else) which is on back order at the Salt Lake Dodge dealer. I have to take the truck there again once the radio comes in.
Wow, that stinks. I was in the same boat as you. I had 750 miles on mine, and it had an MSRP of $73,900 so it was tough to convince myself, and especially my wife to cut it up and of course spending $8k+ to do it.
I had two other issues with fit and finish. Days after I got it home, the fender flare started to come off on the rear. My truck is a dually, so it may be different than yours. Apparently it's partly held on with adhesive. I brought it to the dealer for an oil change and had them look at it. They ended up replacing the adhesive under warranty, apparently not noticing it's not the bed it came with. Gave them the ability to charge Chrysler for some labor I suppose. Mark said he'd pay to make it right, but he didn't have to.
Second issue was the bed they provided was barely dented on the top rail passenger side under the plastic rail cover. Like someone hit it with a ball peen hammer, or they dropped a bed on it when they stacked them in their yard. All I noticed when I picked it up was that damn cover wasn't staying down, but didn't know why. Mark thought it was a clip, but he didn't have one and I had picked it up after hours. When I had the dealer check that (when they were doing the adhesive on the fender flare) they were the ones that told me this is what it was (and there weren't even clips). They said they could glue it down, which they did and it's now "fine", I suppose... It was very slight and you can't tell, but it's there and I know it's there.
I'm just remembering now, when I changed my oil a couple weeks back I saw a very slight "wetness" around the fuel filter hose they lengthened. I had just topped off my tank, and I was on a side hill in my driveway. I forgot until now to check that out. Looked like I may need a hose clamp or tighten a hose clamp. So that might be another slight issue you may want to eyeball on yours over the upcoming months.
I will say other than the blemishes, I now have 24k miles on it and there isn't a squeak or rattle and best of all the driveshaft is perfectly balanced, which was one of the things I was worried about. Tire wear seems normal in the back. Had some scrubbing on one of the fronts, but that was my fault as I initially underestimated the weight on the front axle so I was running my tires a bit lower than I should have. The extra length made it drive that much better and the length isn't noticeable. It was a school bus before the stretch, and it makes u-turns just as bad after, but not noticeably worse.
As for it being washed when I picked it up, it was raining all week so they didn't wash mine. This rain could explain why the paint is bubbling now. Ironically I asked Mark when I picked it up if I'd have issues with the paint, and he said I shouldn't. Well... :-/