EDIT: Finished the Gimle missions today - my kid has not stopped talking about Gimle 3 (the great Dralthi turkey shoot; where you face Dakhath) all damn day. It's getting kind of annoying, actually...
Have you ever considered a rule set for miniature combat? I'm toying with the idea of adapting the old FASA Crimson Skies rules for it, would seem like a nice fit. If I ever find anything that resembles time these days, I might try playtesting it with my old pencil and paper group.
The interesting part about crimson skies is that the damage model is less abstract. you basically have a grid overlay of the generic fighter type and use templates to mark off damage. it's D-10 based so it'd fit into the existing rules set. but in a nutshell, when you hit the target, you roll to first determine location (left wing, fuselage, etc) then roll a column 1-10, you then apply the appropriate template for the weapon on the column and mark off the boxes accordingly. Internal hits aren't as random after you've punched through the armor. In fact, the higher your character's gunnery skills, you get the ability to shift damage 1 or 2 columns left or right to capitalize on previous breaches. It becomes a bit problematic on shields, since they are sort of a general armor layer, but you could either just count off the appropriate boxes for the weapon type and apply it against the shields or have the shields act in a similar manner as armor.
I was going to ask about how damage from missiles would be applied to that Crimson Skies SSD for the Rapier. Do missiles follow special rules? I really should see if I can find a PDF of the rules somewhere so I can better understand how the system works; it definitely looks interesting.
Would the internal systems template be pretty similar for all craft, or would some of them have more damage boxes than others?