Why won't my computer get rid of itunes?

I just got a new ipod touch, and it said in order to synch, I had to get the newest itunes, so i did but then it said it couldn't uninstall the old one, so I tried to manually uninstall from "ADD/REMOVE programs" on the control panel but it says it can't find the .msi files to uninstall the applications, so i went directly to the program files through C://ProgramFiles and threw it away, and I was able to remove everything but part of bonjour. I tried to install again and it said I hadn't got rid of quicktime and that i need to do that in order for it to install, but quicktime is gone. I recently did a system restore because of an svchost problem i kept having, could this be affecting it?