Gamera,
Others have helpfully informed me that the knobby clear things should be painted over except for the rectangle area facing the rear of the ship - nice and easy! I was cautioned to take pains to effectively light block the area.
For the warp nacelle "tail light", I put a small swatch of aluminum foil attached with Future to light block the exposed area.
https://flic.kr/p/2gqZdmc][/url]K’tinga-74 by N.T. Izumi, on Flickr
https://flic.kr/p/2gqZsuD][/url]K’tinga-75 by N.T. Izumi, on Flickr
Note mismatch on the nacelle halves!
https://flic.kr/p/2gqZsn4][/url]K’tinga-76 by N.T. Izumi, on Flickr
I was able to work on the model yesterday, and reached a milestone of sorts. The warp nacelles and the side bars on the hangar deck have had their LEDs permanently attached and the parts glued together.
https://flic.kr/p/2gqZsdb][/url]K’tinga-77 by N.T. Izumi, on Flickr
I must confess to a horrifying mistake - boys and girls, when they tell you read the instructions, they mean READ THE INSTRUCTIONS. I didn't pay attention to which light conductor went into each nacelle, so of course I switched them. The parts are handed, so while they do sorta fit switched around, they fit better the right way. I didn't realize this until the glue was on the first nacelle - what tipped me off was that the nacelle end cap's opening for the tail light is slightly offset. So I took a deep breath and pried the nacelle apart. Fortunately there was little damage, so it's just more putty work to eliminate the scars.
It's starting to come together now. Once all the LEDs that must go in beforehand are installed, it'll be all assembly and filling/sanding.