Quick update on this. I talked to the dealer and
1. He offered to replace loader bucket if I want. I'm going to put a piranha bar on it anyway so the only potential issue would be if I have trouble getting it to fit.
2. Box scraper will be replaced with orange one when they get one in
3. I didn't mention the zip ties
4. He asked for pics on the scratches which I sent but I told him in all honesty it's not that bad. I think they'd replace the hood if I whined but I'm going to let it go, I'll certainly be doing much worse to it than that.
5. I didn't mention the dirt/dust
The other thing I forgot to mention in my original post is the tractor had 1.1 hours on it when delivered. That seems a bit much to me for "new" one but maybe that's not unusual and obviously is nothing in the bigger picture.
Very happy with the 2650. Just slightly disappointed with the lack of attention on dealers part, but I'm already over it. It's time to put it to work!