Okay, I solved my dilemma. I went ahead and fished up a 16GB microSD I wasn't using at the moment, formatted it and put it into my switch. It had to format it again, then I turned the switch off and put the original SD card in; it recognized it! So I got cfw running with the new card and ran DevMenu over Hulu which I installed via Tinfoil. On the new card, DevMenu actually loads up after "Install from SD" is selected, so it is something to do with my normal SD card. I ended up installing updates/dlc to system memory since it's not the normal card, which for some reason made me reinstall the base games on my normal SD card, but once I did that they're all updated like I was hoping they could be. I figured even if something screwed up I'd be fine, since I made a complete nand backup a week or so ago before I started screwing with my switch.
Oh, if anyone in the future is repeating this, know that when you reinstall a base game with Tinfoil that it will get to 99% and then "error" out. Although the title is installed properly and playable on the system; I guess it wasn't really gone. In fact, before and after installing the game the same amount of space was free on the SD card. Some header somewhere probably just got messed up and that somehow fixes it. Neat.