I'll point out that all of what we are doing is not fully supported by a truly established company. That being said, there will likely be differences in each users experience. Not all questions and behaviors can be explained, but there is a base guideline on how to get to the end result which is a fully functional emuNAND with eShop support, CIA installations, etc.
I can't explain why Luigi's Mansion shows up in your menu, but what matters is that you have emuNAND access, can update emuNAND, gain access to the eShop and re-download your copy of Four Swords. As long as you can do that, I think you will be okay.