Note, my trick for reducing the performance impact of high ROF cannons is to clip their lifetime and increase velocity. Talking real world muzzle velocities and accuracy, the lifetime should be manageable. My idea is to cut rounds off at a range at which the vast majority of them will miss the intended target anyway. Since CIWS systems are AA weapons, the range won't be all that great. Same with fighter cannons, which would have an added bonus of not being used too often, and in very short, controlled burst. IRL, it only takes a few solid gun hits to down a plane (getting them, on the other hand, is quite a challenge).
Regarding realism of FTL jumps and starships, I already have an idea for this (actually, it's the fighters that are the hard part, warships are easy to justify). Ideally, I'd be able to do a mod outside of SS universe, but since that's a long way off, I'll start with smaller things.