I solved my problem. It was so stupid- hours of searching and trying, and the answer was simple. I'll share for your entertainment:
Do you know that file called CampaignData.txt? I found it, and instead of editing all the original files, I had been making copies with new names (so they'd all be at the top when I looked for the files). In that file, you can select which files are used for the data. I did it for stores, new purchase ships, bitmap effects, character stats, components, etc, with no problem.
Appearantly, it doesn't work for Main_ComponentConfigurationSlotsPlayer.txt. When I renamed the original file and changed the name of my modded one, it all worked.
Gosh, did I find a bug?
Well, I hope you all get some entertainment out of my suffering!
Miyoshi