I'll put together a quick patch for the simple fixes, but torpedoes, upgrades, and Stars of Inequity will take more time.
For the Cargo Bay, there are no official rules for a cargo hold component available to the Grand Cruiser hull type. I'm not sure if that's just because they didn't errata the Compartmentalized or Lighter Bay variants when Battlefleet Koronus was published, or if that was intended as Main Cargo Hold was never made available to non-Transport hulls. You can edit the Components spreadsheet to include the option for Grand Cruiser hulls or change the existing row to All hull types, or add fanon/homebrew versions to that spreadsheet.