Here's the permanent fix for your conundrum - at minimum, always partion your drive into two partitions; install the OS and apps on one, keep your data on the other... Preferable is using two drives, one for OS and one for data. That way, your files are kept segregated from your OS and application stuff - so if you have to do a reinstall, you never have to worry about data loss - you're just out a couple hours of installing!
I run nine OSs off fifteen partitions, and for every single one, the D: drive is "Data". All my systems are set up to see the same IE favorites, the same Outlook PST file, the same My Documents, the same cookies - 'cause they're all on that single data drive!
The situation you are in is pretty much the same as all my 'new build' clients have - they have an old drive, with the OS and data mixed, and some of the data inevitably lost somewhere in folders they've forgotten creating. In most cases, what I do is put 'em in a 1Tb drive, partition it with about 100G of 'system' partition, which is more than they'll ever need; make another partition that's the size of their existing drive, and whatever is left gets used as 'data'. (I won't go into the system backup partion for GB's eXpress Recovery feature, but it's in there too...) I install the system, and whatever programs I know about, then I hook up their old drive, and transfer all the data I can find to the data partition, which typically amounts to copying 'My Documents' folder and all its contents... Then, I image their old drive to the extra, 'drive-sized' partion, so that if there's any files I missed, they aren't gone, they're just wandering around somewhere in the mess!
I'd do the same in your situation - get yourself a nice big shiny new drive (they're getting absurdly cheap - I thing I paid under $70 for the last 1Tb I ordered - and ½Tb's are down under $55!), and do the same. Do your new OS install to one partion, copy your data to the other. Assuming you know where all your data is and your existing drive is over 6Gb, once you've moved it all, format the old drive (using the default 4K blocks...), and move your swap file to it - you'll get a little bump in overall system response when it gets crowded and starts swapping...
I tell people to do this all the time - seven has improved things, but you know how windoze is - it's gonna go to hell, somehow, some time!! It's just, well - windoze... That way, when it does, it's not an issue to fret about, or worry that you'll lose the family photos of Aunt Gladys, who died last year - it's just another reinstall!! Another thing it makes ridiculously simple is backing up - you just select the root of the data drive, and let 'er rip!