You can't go all the way with making ships take damage as they would in SFB, but you can get closer than you currently are.
Systems such as hull, lab, armor, security, etc. can be cut in half in the shiplist. Then they reflect how they would take damage in SFB. It does make your ships a lot more fragile, and makes receiving an alpha-strike more dangerous. Disruptors become better sniping weapons. No one wants to walk through plasma anymore.
Systems such as power, weapons, and shuttles can't really have their numbers halved, for obvious reason, so there is only so much you can do..
I've done this with a few ships myself, and it is a lot of fun. There used to be a full shiplist floating around that had performed this process to all the stock ships. (No, I don't still have it. But someone might.)
-S'Cipio