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

Hey all, I recently tried to dual-boot Win7 and Fedora 17, but Fedora failed thus causing me to have to remove it. Well, that was a problem because Fedora put GRUB on my system. I successfully removed it and restored the original MBR so Windows boots. Now I have a bigger problem: the "bootrec.exe /ScanOS" command brings the result "Number of Windows Installations: 0." But during the initial start of the recovery disk, it finds Windows 7 Professional. And the command "ren c:\boot\bcd bcd.old" says there's 2 files or none at all.
I am looking for a way to clean my disk and restore from a system image without the screwy MBR. I was planning on using DBAN(Darik's Boot and Nuke) to wipe the disk and the Windows included system image creator. But after some research, it looks like the image creator will copy the partition arrangements and the MBR, so I would have then done a lot of work to be back where I started. I would like to do a clean install, but with 100GB+ of Steam games and valuable programs and saves, I don't think its the best option. I have a custom-built, so I have no included software and driver CD's, so re-installing everything would be a pain.
So, is there hope for my PC?
(P.S. my PC boots, so that's not a problem)

Not sure I follow what problem you are having.

If windows boots - the mbr is doing it's job fine.

How do I back up my system without copying the MBR

Try macrium free to make an image, it gives you option of whether to restore the mbr when applying the image.

http://www.macrium.com/reflectfree.aspx

Well, it isn't really a problem now, but I see it becoming one in the future if I ever need to use start-up repair.

When I perform a backup, what settings should I choose? Should I back-up the 100mb partition? And should I allow the saving of the MBR or not?
Thanks!

Yes, you would back up the system partition as well as the o/s partition.

I think it backs up the mbr automatically (last time I looked) - but gives you the option of restoring it,

I see they have just released an updated version. They seem to do that every couple of weeks.

I think there is a tutorial in the tut section - Imaging with free Macrium

I don't think you will need it - pretty obvious how to do it.

Thank you so much! I have been in quite the tizzy for a few weeks now wondering what I should do about this! I never knew it was this simple
Now I know what to do!

Now, will I have to use the Windows Recovery disk to recreate the MBR or will it be there already?

It is there right now - unless you do something to it - it will stay there.

I meant after I cleaned the disk and after I restored from the disk image. Sorry for the confusion!

There is no point in re-imaging from an image you make now. Even if you clean the disk the image will replace what is there now.

What is it exactly that you're concerned about?