Your comments are really got me thinking, that I need to move a lot farther out of the box.
I sketched this out tonight... I think this is what I'm going to go with.
So, the big bulb is the habitable area of the ship. Decks are oriented perpendicular to the direction of travel, as Christopher suggested.
The saucer part is actually what I'm going to call the Electromagnetic Force Field array, which acts basically like a deflector shield. No habitable area in there.
The nacelles of course, made larger, and the matter / antimatter reactors are below.
I also plan to have some fusion rockets at the rear, for backup sub-light, or maneuvering.
This is all really rough, but what do you guys think?