Okay so I figured it out.
The issue is that no one takes the time to explain that FLASHEFI is only usable in Windows 98, so what you're doing is booting into Windows 98 from your flash drive, then using command prompts to run the FLASHEFI software.
For future users having the issue.
Follow the instructions in the first Quote box
http://forums.overclockers.co.uk/showthread.php?t=18404556Then copy and paste the three files, not in a folder, onto the flash drive and then reboot your system, set the boot device priority to the FDD and when "Loading Operating System........." Comes up just let it go for as long as it has too.
If it works correctly you don't have to do anything, it just starts the tool and flashes everything for you.