Mobo upgrade: Re-installing windows on a non-bootable hard drive (without formatting)

I just upgraded from a roughly 10 year old MOBO/CPU to a ASUS M5A99FX Pro 2.0 / AMD FX8350. I am running Windows 7 x64 Enterprise

I've read that even though it is not recommended, some people are able to install a new motherboard/cpu without having to format and re-install Windows.
This unfortunately did not work out for me, probably the combination of my hardware being so outdated, and switching from an intel to an AMD processor. When I start the computer I get to the Windows animated logo for about 10 seconds, then the computer restarts.

I don't mind re-installing Windows 7 If i can choose the "Upgrade Windows" option, which installs over everything and keeps all your files. If I select Upgrade when booting from the disk it tells me I need to run windows, and then select this option.
Formatting and doing a clean install is not an option right now. I have roughly 1 TB of files and not enough space to back them up.
I've temporarily installed Windows 7 on a 450gb hard drive, and all my new hardware is working great.

I need a solution to Re-Install windows on my 2TB hard drive which I can not boot from, without formatting it! Is this humanly possible?

By the way, I've tried launching Window's stand alone startup repair, and also the boot disk's Repair My System but neither helped.
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More about mobo upgrade installing windows bootable hard drive formatting
  1. How many partitions have on your disk?
    If you have 2 (C & D, on D is all your data), you can format only C, install win....
    D partition will remain untouched, with all your data.
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