Okay so I haven't been able to solve the "Reloading Bootmii iOS..." problem no matter what I do, but I decided to try to see what happens if I use the emuNAND generated from ModMii with USBLoaderGX. I set the EmuNand Channel Path and Save Path to nands/p1_us. When I try to boot the NAND from the features menu within USBLoaderGX options, I get a black screen. I powered off the Wii after about 15-20min of waiting and went back to USBLoaderGX.
Instead of trying to launch the NAND through the features menu, I tried to launch the games that I had installed to the emuNAND from ShowMiiWads and THEY WORK. That's all I really care about. The entire goal was just to get WiiWare and VC games running from USBLoaderGX and WiiFlow (which I haven't tried yet) without having to install to the real NAND. I tested games that are supposed to be problematic without neek mode such as N64 (Super Mario 64) and WiiWare games from other regions (Akumajou Dracula X: The Rondo of Blood) and they all seem to work fine.
Now I have two new problems which should hopefully be easier to solve:
(1) Some of the games don't have their title, just their Title ID. For example, Castlevania: The Rondo of Blood is listed as QAPN in USBLoaderGX. Is there a way I can change this? I don't see any option for it in ShowMiiWads.
(2) Some of the WADs that are probably necessary to run the games show up in the games list, such as NEEK2O. I haven't tried to remove this WAD because I assume it's a critical file. Is there any way I can exclude it from the games list in USBLoaderGX and WiiFlow?
EDIT: It's not fully working like I thought at first glance. I didn't realize that only some games require neek. The games that don't require neek work perfectly (although they take like 15 seconds to start and the disc drive is flashing blue during this time), but Castlevania: The Adventure ReBirth freezes on black screen without neek and, if I enable neek, I just get a permanent black screen. Some N64 VC games don't seem to work either. Smash Bros. freezes on the "Classic Controller Required" screen, and I haven't been able to test it with neek since I just get a black screen when I enable it. Ugh.