You actually more or less pointed me in the right direction bound4earth!
I set the hdd with windows 8.1 as active and removed the drive with windows 7 on it. Booted my installation media so I can get into a command prompt, re entered the Bootrec.exe commands and this time they took properly. Then told the Installation media to repair startup and Voila! I'm currently running my Windows 8.1 installation WITHOUT the win 7 hdd installed! Thanks a bunch!
Sorry about the late reply, not easy to do remote trouble shooting through forums. Glad you were able to solve the issue finally.