As i said, i messed up the last update (the last before that was ok). The errors u found are from the ship hulls i think, when u change a hull ship in the in-game editor from a ship already done, it seems that the editor mess up the hull section. U can solve the issue redesigning the hull section of the ship, but as i said, im not going to release anything by now, not till i have the complete first part (The Earth Alliance) finished, tested and really with no bugs.
About the weapons issue, it seems that the turret mapping is missing (something that i cant believe is already happenning) but i cant tell u how to fix that, cuz i am re- designing the whole part of the mod, and some weapons are restricted to the Colonial Side, and the accelerated chaingun is one of em. And all the values that surrounds the turret mapping are changed. I recommend u to have patience till i release the new redesigned part of the mod.
If u can, give me a link to the original mod (the one u have and is giving you that errors) and i will look into it and fix the issues (this will be fast). I cant do anything without the original mod, cuz as i said i changed weapons, values, references and i cant do anything based on the mod the way is right now.
And yes, of course i will include the Utopia Star Base (the Federation starbase) from the New Era Side, the Babylon 5 Station from the Colonial Side, the Omega Class (Alias Agamemnon) and some other ships that were missing in the first release.
I only can tell u guys to have patience, i dont have enough time and, although this mod is not too extensive in weapons, modules and so on, i am really trying to make a good mod, very balanced, with good turrets, with decent sprites, etc.
Yea i have a lot of ideas to the Borg Collective (including of course original vanilla races assimilated xD), and mostly of em are going to be designed from scratch using sketchup, so the Borg Collective will be a extensive race with a lot of hulls. And after that… the rest, the outsiders league. But all of this will be the next year, right now, i need to focus on finishing the Earth Alliance side.
About the fighters repaired with no shields… it is supossed that once a fighter goes into the carrier bay, the shields are gone, and as u said, the carrier bay is designed to repair armour and critical systems (of fighters), no shields. Maybe it is a game bug that if a fighter enters the carrier bay with the shields still intact (something almost impossible cuz the shields are the first thing to be damaged) that fighter just loses the shields forever.