Thanks for looking into my build!
-You could paint the interior before drilling. I did after because since this is my first FO work Im trying to cover up all the possible areas that could result in light leaking. In my case the paint did not clogged up the holes, results may vary.
-I did not used any particular method but decided to let the strands show me the best place to accommodate them according the internal arrangement of the model structures first. The max of fibers depends on the light source and the diameter of them. Im using 5mm LEDS with 0.5mm FO all tucked inside an 1/4" clear vinyl tubing. My guess is you could fit between 25 to 35 fibers inside easily per LED. Sometimes I stuck just a few FO per LED depending the location. Its a learning process.
-I did not use a pattern. I went randomly into where I wanted a spot of light to show. A pattern will look weird. I did it just as the guys at ILM did it...by ear! LOL!
-I thought for a time to use a 12v external source. But Im leaning to use a 9mm battery outside the model itself, probably hidden in in the base. The 9v source seems more than enough! The LEDS really light up super bright. The blue ones for the engine can be used for a weird blue flashlight if desired. They can light up quite far into my backyard! I will have two circuits, 1 for the whole little light of the model, including the bay and one for the engine. The reason is that I will use a dimmer for the hull and bay lights. Dimming the lights makes them more to scale and better when photographing the model since photography is another hobby of mine.
Hope this helps.