To sum up, anyone having a problem loading their modded save should do the following steps:
1) Start a new game and save it at the first save sphere onto a memory card or hard drive.
2) Put the file you want to mod on a USB or SATA and mod it, rehash/resign and stuff, then load it back on.
3) Start up the game, choose "Continue", select the memory card or hard drive that has the unmodded save file, and select "Load".
4) When it shows you the unmodded file details, hit X, (in the bottom right corner, it says X to change storage device), and select the USB or etc. that you have the modded file on, and load it.
There you go. =]
Any advances to an update, Sephiroth?