Figured it out. A friend mentioned to try rebooting, after laughing at him, I then said aww fuck it. Gotta try anything at this point.
Well it worked.
For those that run into the same issue, here is what you need to do:
1)Attach drive via usb or to IDE/SATA chain
2)After booting log in and modify drive permissions to allow for your user to have sufficient permissions
3a) Run AV Tool as Administrator
4)Scanning should work fine now.
5)When finished shut down, and disconnect drive
6)Reset permissions back to normal within the formerly infected OS
7)Run AV tool native to system.
Should be done and ready to rock.
HTH. I was only missing the rebooting part, so I am not sure who else ran into issues here as well.