I think the front of the ship should the the shuttlebays, not the way you have it now. I'd bet that once you weld those two end pieces as one part, a WADE-style deflector would look much cooler. As for the other end, how about an attachment to haul a FJ-style container, for supplies and possibly extra capacity? Heck, I'd bet that at the size you have it, you could fit three or four of them at the back end. Please try to rescale the windows though, because the best kitbash jobs aren't kitbashes at all.
This has potential though, keep it up.