Huh. This isn't dead. Truth be told, I had been completely certain you were drunk or something when you made this thread, and that it'd quietly die pretty much as soon as you sobered up. Guess not. Uh. Good luck, I guess, I certainly wouldn't have the will to complete a project like this.
One thing, I highly recommend that you pursue an episodic nature, following the missions. Most missions had very clear plotlines, and obviously they had nice neat starts and finales. It also just gives a very nice structure to the story; main arcs (missions), which would be more serious and focused, with short fluffier segments between to develop the characters (on ship bits). It would have a pleasing tempo to it, if done well.
I also feel that you should really try to include most stuff that isn't just completely worthless, even if it's tonally inappropriate or jarring. When you're done with the drafting in, uh, three years, the project will likely have evolved in a different direction. Maybe it'll be more comedic, more tragic, certain characters will feel more or less important, or something else entirely--regardless, you'll have a better idea of what should be cut after you've reached that point. You'll likely also have quite a bit of feedback from readers on what early parts they liked, and which they didn't, which will be invaluable.
...I can't resist asking. What, if anything, will you do with Tinker? I'd presume it'll fade into the background and become just a minor side-element that's mentioned offhandedly, but I'm curious all the same.