Well there will be an offset off of the blue deck lines which will be similar in each deck, thus the height on each deck of 8 feet will probably drop by a little. The bridge may seem a little squat, but the floor area does sink a little further into the deck below which will be where the main computer will be located in the saucer section. (backup will be in the main hull)
I've finally considered that this will be a starship that comes after Voyager/Enterprise E and right before Spock heads back in time..... thus computer hardware and much of the innards of the ship will be more compact and reduced in size, aka: simplified.
I was about to start working in Maya this weekend, but forgot to email myself the newest file of the starship to my home system.
Will be a little while yet, but the first thing I believe I'll be working on will be the warp nacelles.
Worst case, if I didn't make enough space for all the decks and electronics, is to remove 2-3 decks and re-adjust, thus the overall shape and design should be sound for going ahead with 3D modeling the basics.