Alright, so I had a thread in the main forum with a bunch of this stuff, but with the recreation of the painting thread, I figured I'd move some of my stuff over here.
As I've been pulling ships apart, I've been trying to remember to take some pictures of the inside to hopefully assist others in how these come apart. To start things off - (one of )my current project(s) - the Ghost!
I just started this on Monday, so I'm not too far along. Thus far I've managed to tear it all apart and get one of the engines carved out for lighting purposes. Here it is in its disassembled state. Note that the sides on the bottom disassemble as well (where the airlocks are) - it appears to be a single piece spanning the width of the ship. Also, the shuttle itself was cut off - it's part of the center section.
I did find that it was more difficult than normal to pull apart, but I believe I did it without hurting the model at all. After popping off the top section (which was by mistake, I wanted to get the engine section off and it all came off), I put some clamps in the inside (the gray ones at the top left of the picture) putting stress against the two halves and put it in the freezer over night. This loosened it up enough that I was able to apply pressure next to each post and pop them apart.
From there, I dremeled out the back of the engine diffuser to get the center section detached without harming it, and cleaned it all out. A well trimmed bit of milk carton was glued back in place, and the center section of the engine glued onto that. Next up was drilling through the length of the engine, I had to go in from both sides since my bit wasn't long enough, and then slowly and carefully widened it up. It's about as large as it can get right now, but my 5mm LEDs don't fit through, so I have some 3mm's on order. In the meantime, proof of concept at least works!