Messed up MBR, How do I back up my system without copying the MBR?

The "/ScanOS" command can't find a windows installation, which worries me. I've tried everything except switching the sata ports or doing a clean install.

This is not uncommon and can be disregarded if you have no other problems.

I would run Startup Repair a few times from the WIn7 installer or Repair disk to know that your boot files and MBR are sound. It runs many tests, commands and if necessary fixes. This is also the best way to recover from GRUB in the first place.

If you post back a screenshot of your Disk Mgmt drive map and listings using the Snipping TOol in Start Menu we can look it over for you.

Here's the screenshot from my disk manager, the 1mb partition formed after a few installations of Linux.

Another quick question: I recently looked in my System Reserved partition to find 2 BCD backup files, should I delete one both or none?

There is plenty of free space on the SysReserved so unless someone else knows better I would leave it alone.

If there are no performance problems, then it looks correct and should be good to go.

If there are performance problems, post back to let us help you resolve them.

Here are generalized Troubleshooting Steps for Windows 7 which you can practice now to become more familar with your System.