After spending a full day on this, we (Your IT Pro and I) finally got it to boot by restoring the registry from a backup which windows keeps.
Boot into Windows Recovery command prompt and do the following:-
1. CD C:\Windows\System32\Config\RegBack
2. MD Backup (MD Is the command to Make a Directory)
3. Copy *.* Backup (copies all files in the folder RegBack to the Backup folder created in step 2)
4. Copy *.* .. (copies all file from the RegBack folder to the folder below, Config, overwriting them)
Hopefully, this will allow your server to boot.
Updated 17/09/2016 and 14/12/2016: Updated the instructions for clarity.