|There are various anti-virus options that can be run - without booting into Windows itself; they run from a DVD based OS. Kaspersky Rescue disk is but one of several (all free).|
There are also other utilities to the same end that manage to sniff out a lot of pests that hide within a booted Widows OS.
Rather than intrude (from my side) and possibly confuse the situation more than it is just now... I suggest you persevere with the path/approach from JohnW as he will help you get rid of what ails the system.
I doubt you will need to re-install Windows if you are willing and able to persevere...