Apps folder...I feel kinda dumb now At any rate, thank you.
I actually got it workin and it wasn't the cIOS. Wiieye's suggestion did the trick, however it didn't work the first time because it was a bad image. The first image I used was from a double layer backup of the game that I didn't burn correctly. I read somewhere that the movies in this game were on that second layer so I guess that's why the image copied over and Free Mode even worked, but Story Mode had cut scenes and that's why it wasn't loading even after I changed the setting to 222 in USB Loader.
So after finally getting WBFS Manager to work (whole 'nother story) I copied the image directly into the external HD and finally got it working.