My suggestions come from looking at things from a game perspective, so they are understandably lacking in internal game-universe logic. But let's see what I can do :
APBs vs. TLs - both use magnetic acceleration to fire packages of energy contained in magnetic 'bottles', but the content is different (antimatter for APBs, plasma/photons for TLs).
Regarding SW warhead weapons, I agree that there would be problems. Perhaps we could 'grid' them to require Missile Weapon
and Torpedo Weapon technology (maybe Physics 1-3 too). I'll think of something and post a proposal here.
If we give the Empire other fighters first then the Fighters tech area will have to stay extended out to level 5, as it is in your current files. That being said, I agree. On a timeline basis, TIE fighters were developed before gunboats, so I like your other idea better - make some of the lowly fighters like the Pinook, CloakShape, even the Z95 available to all. The better 'other' fighters can be kept in reserve for when we add the Black Sun / smugglers as a separate race.
Maybe we could 'grid' the Gunboats so the Empire only gets them after they have developed fighter-sized shields.
This link here has some excellent craft pictures, by the way, including all the X-Wing Alliance fighters.
Regarding the Force, I have some ideas, but I'd rather concentrate on non-Force tech first. Once we have that coded, we can spend as much time as we want discussing Force stuff.