I think you're missing the point about what a customizable card game is. Did you finish reading the instruction manual? You need nav points and a carrier (which don't even really count) to set up the playing board. Then you need some fighters, since this is Wing Commander (and even that's not absolutely necessary!). If you have fighters, you determine what number of specialized weapon systems or ace pilots you'd like to beef up your deck. You have to balance this versus how many maneuvers and battle damage cards you want. Modifers, secret orders, medals and other cards deepen the strategy further.
If you want to stack your deck with 60 Hellcats, that's fine. The game will suck, but you can play that way. If you want to take two fighters, two pilots, two missiles and 54 maneuver/battle damage cards, that's fine too. You'll lose pretty quickly after your first fighter goes down though. So there's no answer to how many cards or exactly which cards you can take. That's half the strategy of playing a CCG (and discussing the different possibilities is a great debate).
