As I see it, you should have formatted the old Windows you had - once it's there, it's there, and it won't give up - it's actually a good quality, preserving the fundamental.
I think Ralph is on a good trail. Personally, I would use something like
http://www.aomeitech.com/aomei-partition-assistant.html or
http://gparted.org/download.php to clean it all, everywhere, thus get a truly clean install.
Fixing things may quite often take more time than to start from beginning. Not really sure about it, but I give my standard advice: have System in one place, and have personal files another place / partition. That way, when you need to fix System, you need not to interfere with personal stuff.
Best of all.