OK. I have a server running Windows Server 2008 R2 SP1 bla blah.... So it was having some HDD issues (I guess a 9 year old hard drive isn't the best thing to run a server off of.) So I ran chkdsk and it found some bad sectors and it erased some files that i thought looked like system files, but I had no choice in the matter.
Sure enough, windows won't boot, it just constantly restarts.
Push F8 on boot and hit "Disable Automatic Restart on Failure" so you can see the blue screen. My BSOD said the following:
Stop Error 0x00000074
After googling this, it pointed me to a bad registry.
The logical step in the matter is to use "Last Known Good Configuration" on the F8 menu, this option did not auto-reboot with a BSOD like before, but it never actually loaded up Windows. So after cloning the HDD, (I used Paragon Hard Disk Manager, but you can use anything), I had a few problems with the BCD file. So i booted off a Windows Installation disk, loaded a command prompt, and typed:
It says D: because it found C: as my 100MB System reserved partition, the one with the Boot partition files on it. After bcdboot did its job, my bcd file was rewritten correctly. This may be oversimplifying things because i've had so many hassles with the BCD Files, but you can check how things are going with BCDedit /enum all.
Now I was back where I was before, with the registry still broken on the new HDD.
After trying about 50 different things which I won't get into, I stumbled upon a CD I had used a few other times called "Super ERD Commander" (I believe I was using version 2005).
I assumed I could boot this and then check the registry files directly to do something to them manually, but to my surprise, as soon as I booted Super ERD Commander 2005, it tells me something to the nature of
"Found a corrupted registry hive, Fixing it."
So I reboot, and voila, Windows boots, and everything is fixed! No lost data or anything.