Michael, you will need to make a small cut from the bottom of each pylon half in order for you to put wires through to the nacelles.. I would also suggest putting a hole on the top section about 1cm wide on the top section in the middle of where the neck will join to allow wires to go through to the neck and saucer..
I would then build the top of the secondary hull, with the side panels and pylons first, putty, sand, and then paint.. once done, you will then be able to feed your wires through the holes in the bottom of the pylons to the top for later.. Although difficult, do not add windows until all paint and finish work is completed....
Build your power sorce in the bottom section, and if you plan to add a lit shuttle bay, then this will need to be tight and neat.. I think you will work the rest out.. I would also join the neck to the secondary hull before painting also, so you can fill the seem to avoid light leakage, and can also putty if needed.. I painted my neck seperate, and had a hard time joining it, which meant having to go back and clean up.. also you will need to shave your neck pegs, they are too thick..
The Nacelles, and the saucer can be done seperately!.. Another reminder.. Make sure you have all your clear parts put in place before you put your side pieces on the saucer.. They are a pain to remove once in place...Always double check!... I had actually planned to light this thing in the first place, but later decided against it, and had it all planned out... Hope this all helps...
Chris in Japan