Questions and Opinions on Rigs

For the Ram 3500, there is an available factory air suspension. It is more expensive than available air bag systems out there. But since it is a factory item it would be covered by warranty. Thoughts on this?

It depends. if their system simply air bags, then no, not worth it.

Both trucks can be optioned with dual alternators. How much use are these for the TC? Can you use them to charge batteries or say run the fridge or AC while running down the road?

With a good solar system, your camper will charge batteries going down the road AND standing still if good sunshine is present.
The truck alternators camper charging ability is limited by the small wire in the camper cable - truck charging will be insufficient to run fridge or AC.

Factory Upfitter modules. Any use? Extra Factory auxiliary switches. Any use?

Yes to upfitter switches. You might want to add a rear view camera to watch that towed Jeep. Or additional lighting projects in the future.

Axle ratios? Can I get by with a 3.73 or is a 4.10 more realistic for the AF1150 with a trailer behind?

3.73 with a diesel engine will do the job for you.

That AF1150 will put the rig at, and mostly probably, over the trucks GVWR - so be aware of that.
Concentrate your resources on upgrades to the sway bar and shocks. Possibly consider after market wheel and tire up-sizing.