Yeah I'm not sure how that will work, without dropping the floor to extend the depth. You'd have to pop out the floor boards, move the joists & flooring down about 6 inches, and patch in the walls. As it stands right now, I'm not sure what you could use for litter that wouldn't get kicked out. Dropping trays under the roosting bars would definitely be a good idea.
As for roosting in the rafters, they're gonna do it anyway. My coop has rafters high enough for my 6' tall husband to walk around in comfortably, and we've got plenty of roosting bars the are about 3-4' high, and one of my Easter Eggers still likes to roost in the rafters every night.

I wouldn't worry about that so much. Judging by the look of your trees I'm assuming you're in a warmer climate than mine, so you should be OK.