this seems like a really cool idea.
so you have components that have requirements to work (need power for the railguns) and you have a system whereby commonly used techs grow in level faster (use a lot of railguns and you unlock a better capacitor)
i think you're game should have a 2/3 dependency on contracted work to accelerate technology levels. the over 1/3 should be created by laboratories and directed towards special techs. this way players can force breakthroughs in a new tech and begin building ships wth that tech to advance it further. just to stop a player from getting angry because he cant get his first laser to start down that path.
this game seems like it would work best in a game where there is a small scale (5 solar systems with 3-4 planets each) and with realtime battles on these planets (which in my opinion is the only way to elaborate on ship components beyond "this one is cheaper and does more damage" galactic civilizations cheated me with eye candy.
another suggestion i have is that certain components must be "linked". for instance a Fusion reactor needs to have tubes built that connect it to drive plasma storage. this would also give ships things such as range, ammo, effective runtime. there could be different types of the same general component that each give tradeoffs (spherical reactors give better power but have short lifespans and are prone to malfunction.) this would add to the importance of design, and give each players empire a special "tone" (one empire has a lot of powerfull ships with short effective range meant for deffense, another empire has super fast ships sporting a single cannon.)
it might also be a good idea to have "realistic damage" whereby weapons will penetrate ships and damage components, so placing only one feul line and leading it along the outside of the hull may save a ton of cash but it will make you're reactor vulnerable. this will further increase the importance of good design. it will also mean that ships designed for deffence may be more willing to place engine components near the outside to protect their presious mass driver, but pirate ships would probably tack on their weapons with duct tape so that they can run if things get "dicey"
spliting the ship into a grid would be a really good place to start. i wouldn't limit the ship to a hull simply because it forces players to limit their creativity. (some players want death stars and why should they suffer for it?) i feel that most of the problems with balance in games where ships are designed by players can be solved with appropriate attention to metagaming and ship design. giant death stars may look bad but having only one gun makes them extremely vulnerable to kamakazi ships.
another idea i had was that you would have two types of research upgrades. components and upgrades. where components are actual objects that can be placed in the grid, upgrades are things such as a cryogenic pump for a nuclear reactor that increases reactor output by 5% this wold increase the perception of advancement without rapidly obsoleting current designs (a serious problem with most 4x games is that you can never build a decent navy because the ships are useless by the time they are built.)
i have a metric ass tone of ideas that i can contribute if you want. i had put a lot of thought into a game that serves this function and would love to see someone proceede with a game.