So I went back, updated Nintendont from my old version (since I hadn't touched GC games for a while), and now it seems all is working, using USB Loader GX as the menu for my GC and Wii games, both types on the same drive, same FAT32 partition, though it was very particular about which USB port to use (if console is lying flat, it's the top USB that worked for me). It even has autobooting working (which is something the last version didn't like).
Though updating Nintendont now has ULGX complaining that it can't verify it, I can load it anyways and it still works. The one thing mentioned on the GBATemp page for Nintendont though is that I can only have one drive connected for it to work, meaning I can't have both my GC/Wii stealth drive and my Wii U drive connected together at the same time. I believe I can have both connected if I just want to play Wii games, but not GC games. Well, I can always just swap drives connected through my Y-cable when I want to switch between the two (as I also use an ethernet adapter, so I'd only have one port left anyways, and my USB hubs have been having problems lately).