I was actually going to post a link to that excellent build thread (beautiful stuff there!!!), but got sidetracked by something shiney!
But, to the question at hand...paint up the interior first (obviously), them build up your exterior, as much as possible...with the exception of small pieces that can easily be knocked away (antennas, probes, etc)...I glue (with just a tiny dab of CA) the small bits on a piece of scrap sprue, and paint them seperately, at the same time as I paint the model...those all get glued on after painting, gloss, decals, wash, weathering...then the final flat clear coat after all is in place.