Looking great !!!!, you are definitely getting it all figured out!
I'm not sure if your cab is sitting same height from the frame as mine is but you've probably noticed there's a ton of room above the transmission.
I Went with cutting the hump out completely and made the floor completely flat,(kinda like the older caddys were) and so the 5 spd sticks thru the floor by about 2",
the rubber dodge stick bellows was plenty big that I could cut a big enough port that the trans could never hit the cab!' ( food "for thought anyways).
I don't have a transfer case lever thru the floor, instead I'm building a linear shifter......meaning cable operated in/out style.under the dash and parallel with the floor.( I'm in Canada eh so it's 2wd for 6 months and 4wd for 6 months)
I'm almost done my build except for powder coat on the deck and running boards and some upholstery,namely seat and carpet.
If you need some pointers then I'm happy to help.
Cheers......