I would not take two weeks to get to Glacier. I might do Yellowstone/Tetons before Glacier depending on the cold Wx forecasts... Yellowstone can be colder than Glacier. I would do CO (higher elevations/cooler) before AZ... AZ cooler at the end of Sept. We do three months out West without reservations during the summer months so finding sites in Sept will not be a problem.
We are doing the Albuquerque balloon fest in early Oct and will be doing much the same as you and at much the same time, but leaving off Glacier. I'll get to WY in 2-3 days and spend 7+ days there then south to CO for a couple weeks and then west to Moab, then Zion/Bryce, and then N Rim before Albuquerque.
I would suggest getting a small generator and start staying in USFS CGs several days/week. Often this will get you closer to the sights and save some money.