Wow, they really do take a lot of space! I wonder why? That window is really small.
My bus has just one air intake plenum on the passenger side, and even that is smaller than each of yours. Are you sure they're air intakes for the engine itself, and not ducts for the cooling system? Does that Amtran have a rear-mounted radiator?
I have a queen-size bed in my bus, but it goes back only as far as the original rear seat's backrest. My bedroom extends forward three windows (but Crown's windows are much wider than other buses'), with plenty of room at the foot of the bed to get out of it easily. Just bear in mind the thickness of a mattress on top of the bed base - with an 8" to 10" mattress on top of the rear shelf's level you may be sleeping uncomfortably close to the ceiling! My bed's base is level with the rear seat bottom, a lot lower than my rear window's shelf.
John