Honestly I think it's not a big deal gunboats and crusier can use the 160k shield; the hull difference is astronomical. Fight a stock gunboat (with the 160k shield) vs a stock battleship with say a 40 or 80k shield and the battleship will still win hands down. A 350k hull vs 50k is a real no brainer.
There is no real way to balance large vessels against a fighter; the moment you do there isn't much point to a capital ship anymore. Good game, thanks for trying! Move along to the next mod on the list.
I agree with daedalus on the issue of adding levels to cruiser forward guns. The system wasn't designed to deal with massive energy bursts over time. I think it will be possible to put the cruiser forward gun on a fighter with 4 nomads and say a missle of choice. Guns will fire if the ship has any energy available; overload a medium range fighter or freighter and you will still have at least one gun always fire when you are out of power.
Four nomads, and a missile will drain zero power meaning the cruiser forward gun fires as it pleases.....