I'm willing to bet you can figure this stuff out on your own. But if you want specific advice for a system:
-First off, keep it simple wherever possible. Something you're only using once doesn't have to be fair, balanced, or a system at all. You'd only REALLY need an elaborate system if you wanted to help someone else DM a game very similar to yours. But on the other hand, making systems is fun... just don't get carried away with a lot of numbers you don't want to track later.
That said, I mean, why not make a little system? That way you know how to resolve things that happens ahead of time, and everybody else is on board and knows what's at stake right?
So... you want to make a suggestion game which mostly involves what the players do with a space ship? Here's what I'd do, based on your suggestion:
-Make a list of parts in the ship, only including what players are going to change or see changed. Say, the hull, engines, weapons, sensors/comms, and whatever miscellaneous stuff.
-To have that stuff get damaged, either give it a hit point total or just say that it's OK/Damaged/Destroyed. Maybe only give the hull hit points. Damaged stuff doesn't work as well, destroyed stuff can't be used.
-For cargo, decided on a measurement (either weight or volume) and just say that your ship can hold X tons/cubic meters, and that each given cargo item takes up a certain amount of that. I would just do one or the other and not both, personally, to keep it simple.
-Modification should be easy! Just replace or change the parts on your ship, attached to the hull.
Beyond that, when you need a simple rolling system fast, base it around dice (best if you have one on your desk, any 6-sided dice will do), or use Roll To Dodge. You're probably familiar with roll to dodge, there's a subforum for it. Otherwise, you could say that characters roll a D6 with a bonus to do various actions. If it's a suggestion game, one character will probably be piloting the ship and doing everything, so have them choose a skill or two to have bonuses in- like, "Shooting, Piloting, Mechanics" or something. Pretty simple, aye? Expand as needed, don't expand where not needed.