Odd. Any ed05 KRC2 should have the USB port working 100%.
Protip: before making ANY changes to this robot, CLONE THE HARD DRIVE!!!! I cannot stress this enough. If you manage to break something badly while making mods, recovery could be impossible without getting original install CDs from KUKA. Especially since it sounds like this particular KRC2 might not be entirely standard.
Also, I wouldn’t be too aggressive about “cleaning” this robot. Just clearing the /R1/Programs, and commenting out the missing I/O hardware, should be enough. GripperTech and SpotTech shouldn’t get in your way.