It's fixed! though I'm not 100% sure what fixed it as I tried multiple things before checking. I'll try and go over everything to help those with the same or similar issue.
I booted into my Windows 7 repair disc and entered the following codes in Command Prompt;
bootsect /nt60 all
then rebooted back into the repair disc and entered the following into Command Prompt;
sfc /scannow /offbootdir=c:\ /offwindir=c:\windows
Finally, I rebooted one more time and allowed it to attempt to repair the start up problems it was detecting.
The only remaining issues are;
- The boot logo/screen has changed from the sexy glowing orbs to the infamous Vista start screen. I'm not sure whether I want to attempt to fix this or not simply because I'm a bit paranoid to mess with anything boot related right now.
- The boot screen disappears quite quickly in comparison to usual, leaving me with a few scary seconds of staring at a black screen before the Welcome Screen appears.
Also, for whatever reason when running the SFC scan it said that some things could not be fixed and to check the CBS log