Tory,
I've done that for a customer, the light bleed through is the issue. ESP where the upper deck mates to the mian hull, the gaps are a real witch to hide, I used white glue and painted. The only way to control it is with Fiber Optics (FO). You need not fill is every window with light about 20% should be realistic. BUT the main two spots that you need to rebuild is the mast tops each had a white light light and the port/starboard nav. lights.
You NORMALLY can't use the kit supplied parts becasue you cannot drill then out, You have to build a telescopetic set of tubes, solder and putty. HOWEVER you can cheat be laying ONE single strand of FO on the backside and paint over then with black first then the brown. On the P/S light you have to add a small piece of styreen to creat the backside of the reflector anyway to be right.
Anything worth doing is worth doing as right or as "best as possible". Look at it this way, you only need to run a few strands a day, soon it wil be finished and you will have the model you realy want. Is there a rush?
Here's one I did but NOT lit up.
http://home-and-garden.webshots.com/album/556497477PLHUEe