First, thank you for your service!
I read in your post that the dealership has major issues. Paperwork processing to executing basic repair requests. Like...the mud flap touching the tailpipe (an easy fix), or cutting down the seat pedestal!? A BIG NO-NO for reasons from safety to liability.
First, take a lesson from your military service and document EVERYTHING.
Second, contact TMC in writing with a specific list of issues (with photos if able) certified delivery...and I would add a section about the dealership and their performance. Dealers have performance standard expectations from the factory. Try to be as logical and factual as possible...think, how would a lawyer write a letter?
In the letter, request/demand a factory POC to help due to the dealer's issues.
Once things get rolling, try as best you can to avoid letting the RV sit at the service center (what ever center...maybe a new one) when they are not ready to do the repairs (parts on hand, space in the shop, etc.). That is when more things get broken, batteries get drained, dents appear, etc.
In summary, the 2014, the Axis/Vegas was a brand new RV model in a rather new segment of smaller Class A's. It rides on a new foundation for a Class A (stripped E350 chassis with independant front suspension, not the Ford F53 used on most all other gas RV's). Because it was the first model year, there were bound to be bugs...but nothing too big, or unable to be repaired.
Unfortunately, TMC allows warranty repairs to be executed almost totally by dealerships and reimburses the dealership. It sounds like this situation calls for "Plan B". Go "up the chain of command" 'cuz "the squeeky wheel gets the grease." Sorry, but the cliche's sometimes fit.
There is a mega-thread here on iRV2 named Letter to Thor that is too big to read with too many off-topic posts. But the original poster found satisfaction from TMC, and it was the letter that worked. Be patient and persistant. Effective communication is the key.
Best luck
P.S. If all else fails, make an appointment and take a trip to the factory service repair center in Elkhart or Wakarusa. They have a great reputation for fixing things right.
http://thormotorcoach.com/contact