No need to give the power supply – or fuel supply – regeneration capabilities. A power supply with a capacity of 1000000000 will hardly be affected by a weapon does 100 energy damage. Increase the capacity depending on the amount of energy damage weapons will do. If you’re trying to stick close to Freelancer’s balance – where ships tend to die quickly under fire – the loss of fuel due to energy-damaging weapons is less critical than if you have ships that survive over long periods of combat.
You could also use WeaponMODDB.ini to increase the damage potential for shield-damaging weapons without, again, negatively affecting fuel supply.
Unfortunately, without knowing the particulars of your modification, I really can’t determine exactly what you need. From your initial post, it looked like you just needed weapons to do shield damage without draining power. Apparently that isn’t what you need, or I mis-read your post.
To easily modify Freelancer’s stock balance – to, say, overall decrease weapon damages (to prevent notable fuel/power drain) and hull/shield strengths (to prevent notable changes to the ‘genius’ Freelancer balance) – I’d recommend writing a simple tool.
inb4 Adoxa pops in with a hack.