Woot I fixed it!
I went and I edited the permissions in the properties of the Sega folder (allowing users/admin users full control). Then I went and changed my folder settings via the control panel to allow all hidden folders to be seen. Last I reinstalled the mod files and copied over the extracted bat and cfg files to the main folder.

i pieced together what to do through here: http://www.twcenter.net/forums/showthread.php?t=89969

Also the bat file still launches with the same code.

Thanks for your help, time to go play your mod.