Installed New Motherboard, now Windows 7 won't start up

Okay, so my dilemma may sound like a simple issue, but its beginning to be quite a problem.
I got a new motherboard for my custom-built PC this Christmas, and generally remembering how to install it, I removed all the power cables running into the board, the graphics card, and other components. Then I removed the 4 sticks of 4GB RAM, and the CPU and heatsink. Then finally removing the grapics card out of the way as well.
I got my screwdriver and unscrewed the motherboard from the computer and set it aside. Next, I alligned the correct holes for the new motherboard (bigger), so that when I screwed it in, they would line up, and put it in.
Then, I found the similar places I remember from my previous board, and started putting everything back together.
Everything fit on perfectly. I went and plugged in the power cable to give it a test run before putting panels back onto the case, and it lit up fine, and all the fans and components were getting power, and then I get a prompt on my monitor asking me two things.

1. Launch Startup Repair (Recommended)
2. Start Windows Normally

Generally I thought to myself, I'll choose the recommended option, since its probably my safest bet.
The startup repair began and started searching my computer for problems, noting that it may take several minutes.
After plenty of waiting time, it gives me an option that says "Do you want to restore your computer using System Restore?" "System Restore can try to restore your computer to an earlier point in time when it worked correctly. This repair will not change personal data, but it might remove some programs that were installed recently. You cannot undo this restoration."
This is the only thing I have yet to try, due to the fact that it scares me. I haven't backed up my computer in quite some time, and I'm afraid I will loose most of my programs and files. So with that being said, I restarted the computer, and when it prompted me, I chose the "Start Windows Normally" option. After a few seconds of it preparing windows, the screen flashes to blue for about half a second, (not enough to even read the text), and the computer restarts back to the two options it gave earlier.
So I began to question that it's possible my motherboard drivers need to be installed first maybe? So I restarted the computer, and forgot to mention that my motherboard name and model pops up and gives me a few options briefly:

1. Press <TAB> to switch to POST
2. <DEL> to run BIOS setup
3. <F11> to run boot menu
Pressing TAB then gives me the option to choose the windows 7 OS and go back to the screen with the previous options shown above, or to run a Windows Memory Diagnostic test. After running the test, the screen flashes black, and again returns to the previous options.
When pressing Delete, it takes me to the MSI control room for fhe motherboard with all sorts of settings that don't seem to relate to fixing the problem.
Then finally when pressing F11, the motherboard prompts me to choose a boot device,
1. UEFI: Built-in EFI Shell
3. SATA3: ST2000DM001-9YN164
5. Enter Setup

Every option basically loads a "booting" screen and then fails to accomplish anything, and results in a black screen or returns me to the previous options.
At this point I am stumped, until I choose the UEF1 ASUS option from above, where it takes me to a screen asking to press any key to continue, then it checks the windows files on the windows 7 installion disc in my disc drive. And then it finally seems to work, and the basoc setup of windows begins, (Country, language, etc.) Then the option to Install now appears, and I click it.

It prompts me to choose the type of installation. Upgrade, or custom. Upgrade is what I want to do, even though my previous motherboard was running windows 7 as well. The custom options says it will not save files, etc, and installs a fresh copy of windows. It recommends backing up first. All of my data is on my internal hard drive, which I can remove, but I have no clue how to back it up now.
I choose the upgrade option and it makes me restart my computer and choose the "Start Windows Normally" option, which I stated before, does not work.

So phew! Finally done typing out the main issue. I have no idea what to do at this point, whether I should choose the option to restore from a previous time, (which will remove programs and such) or to back up my files some how, and do a custom fresh install of Windows 7.
Please let me know if you need any more info, or have any questions!

My Specs:
Z77 MPower "Big Bang" MSI Motherboard
I7 2600k Intel Processor
GeForce GTX 680 graphics card 3.4 GHz
Antec 650 watt PSU
ASUS DVD/RW/Blu-Ray disk drive and player
2,000 GB Seagate internal hard drive
Also to note:
I installed a fan and temperature monitor, as well as two sticks of LED lights, which I hope have nothing to do with the issue.
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More about installed motherboard windows start
  1. You can only rarely migrate a windows installation form one chipset to another. That is your problem.
    Right now all the chipset hardware that your existing windows is referring has been changed and that's causing boot failure because windows cannot intialize your new hardware.
    Ideally you must reinstall windows. You can chose to not format your drive with the new installation and you'll see your previous installation marked as old windows in you drive where it originally was.
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