Thanks for the quick reply.
Those files just finished copying over to the jump drive so I will try that shortly.
Also if anyone else has a similar issue, I found I can also access those files through the windows "Homeshare" program.
I found the drive they were on and right click -> Share with -> advanced sharing otions -> enable sharing.
Then on the new MAC-PC (bootcamp) go to "My Computer" and click "Network" and navigate to the specified drive, and run "FFXISETUP" from there. Granted that only works if both computers are on the same network.
Hopefully someone else finds this useful.