I did something similar - alltoguh I didn't change teh turert numbers...much (So the Typhon and Orion got a total of 28 and the Hecate has 4 more...not big a deal)
The thing is I took stock weaponry and tweaked it. While I did make new weapons, the ship and tables were still usable when playing a normal FS2 campaign. It does change hte balacne quite a bit, but all missions ( except for one) are playable normally.
The one that doesn't work out is the one where you lure Kolth..the cruiser gets tagged by the Repulse becosue of the new big range the Terran Huge Turrets get

A dun experiment, but my anti-fighter weaponry on capship doesn't come close to yours (alltough it should)