Most of that seems technically possible, but would an overwhelmingly massive technical implementation. Bem Cavalgar has a lot of campaign persistence with your and the shivan fleets, but no modularity at all, and that was already pretty darn impressive and probably a nightmare to implement. You should think thrice about even attempting this. Multiplayer is also completely out of the question, it's hard enough to get that stuff working, both technically and playerbase-wise, with retail, let alone such an extreme mod. And that last one, with docking your fighter and sort of making it into a capital ship seems like a stretch.