Right, I don't get what the hell you're on about with booleaning the ports out of the mesh, or deleting the mesh modifiers. But if you can do that without too much effort then that'd be great - you are pretty much responsible for me liking TOS stuff again.
Oh and I thought I'd ask, - I seem to have a really nice Phase II connie on my harddisk that I don't remember D/Ling - is it yours? It has the same phasers and the texturing looks like your style - it's labelled the USS Endeavour NCC-1716