Upfitter switches - big no as they are for the ambulances and such. Are a real pain to program. You do want the Aux switches though which will give you five switches at the bottom of the dash. they can be set to be controlled by ignition or always on and remember the last state. I have these for powering the camper circuit.
Dual alternator - no because you can't have the outputs set to different destinations. If you could, this would be fantastic for connecting one to the camper with heavy wire and it would solve all of the charging issues. I would go with the upgraded 200A alt for the extra capacity. It will have about 160A output at idle.
Air bags - wouldn't go with factory bags but would add aftermarket if needed. Reason is the after market can be plumbed separately which will help with reduced sway and allow separate pressures and that helps with one side being heavier.
Rear axle depends on if you will use tow/haul mode and the speed you drive. If you plan on using tow/haul, stay with 3.73 or 3.42 (my choice). If you plan on not using tow haul mode with the camper on board, go with 4.10.
I just have to ask what in the world are you doing that you carry so much stuff to over load your Ram with only carrying a Bigfoot 9.6? I'm 1,600 pounds under with my Lance 815 which is only about 600 pounds lighter.