According to the spec sheet, it carries 257 shuttles. Out of those, 61 are assault shuttles, 29 Killer Bees, 29 Fighters, 29 Heavy Fighters, and the rest are various utility and admin shuttles.
I can cant the upper portion of the lower nacelle pylons more towards the center of the hull, and reduce the depth of those bays. Or as Bernard said, run the hull thicker between the pylons.
As for the antimatter bottle ejection area, you just completely confused the heck out of me, lol....
But, there will be some reduction in the level of detail, as I'm trying to keep this playable. I don't have a whole lot of time in Max, and there are probably a zillion things I'm not doing that could reduce the polys, so I have to stick to less detail. Some things I'll have to take some liberties on, such as the four things(I really don't know what they are...) which are attached where the hull meets the saucer, 2 on top, and 2 on bottom. I don't have a great view of those, and I haven't the slightest idea of what they are, so those may end up being a guesstimation.
I'm much happier with the impulse drives I built this time. The top is more square than the schematic, but the shape is better. The dome looks pretty good as well. I had problems with the originals, mostly because I don't know how to change the way the poly dividers attach to the vertices. Actually, there's a lot of things I don't know how to do, lol. But the first drives were really bad when you moved them around in the perspective view. The nozzle face was really screwed up.
All in all, it should come out pretty good. This version will be considerably more basher friendly, if anyone should have the desire to use the parts.
It's just about done. Just have to build the bridge, attach the nacelles, and put in the bays. And, if I'm feeling saucy, make a couple of simple shuttles to put in the bays.