Well, it's janky, but I solved the issue my self. I used XBoxHDM to make me a completely new hard drive, using an unlocked 320GB sata drive. FTP works, some stuff don't work, but I was able to load MvC2 off my hard drive, so I'm happy the games work. I'm not a big fan of XBMC for Gamers.
For some reason XBoxHDM refused to make a new hard drive without eeprom.bin. Lucky for me, I had the old 8GB hard drive to the Xbox, and learned you can unlock the drive by turning on the Xbox with it hooked up, then disconnect the IDE cable, and connect it to PC. So, I got my eeprom.bin that way. Even though my Xbox was TSOPed and was okay with unlocked hard drives. iuno, lol.