Oh cool, you got a response from lead art guy David! He's got a lot of good advice there; personally I would probably start out with a transparent layer as the base and/or put the ship in it's own layer (unless I'm completely misunderstanding your process, it looks as if you're simply drawing directly onto the background layer) as this eases that switchover to transparency because... well you don't need to switch over.
On the note of the airbrushing if your program has a blend tool that can also help ease out irregularities in the shading. And if nothing else works, there's always just dithering out the stubborn area a pixel at a time, though that's a bit tedious.
Considering how wonky my colour use is, I don't think I can offer you any advice there, ahehe.
