I've uploaded a new version for the clipping issue. I don't know why it wouldn't load data; I have downloaded the RAR and unzipped it to new folders and everything loads.
Have you edited the CSVs to include custom or homebrew content? Also, what OS?
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.
The reason I didn't add them was because some, like Servitor Crew and Turbo-Weapon Batteries, affect multiple stats and components and I wasn't sure how I could program that in without breaking the current system's way of looking up components and rules. If I do add it in, it will be similar to the backgrounds/packages and not affect the actual stats.
I'm able to scroll through the background screen when long packages are selected. Are you still having an issue with them?