Well I think I have managed to solve the problem.
Using EasyBCD on my alternate installation I installed the BCD onto my formerly damaged partition.
Now instead of booting into startup repair it would return an error saying that system file ""wwfzuyy.sys"" in the System32/Drivers folder was corrupted. A quick Bing/Google search did not turn up anything so, using the alternate install I removed the file from the damaged windows installation. Rebooted, selected the damaged Windows and.....
Sucsess
Booted straight into windows with no problems. I'm now going to run several virus/malware scans to try and see if it is still there.
TorrentG would you happen to know the name of this bothersome piece of malware...