I am always amazed to see people "fixing" a machine over 10..20 hours, but not really getting rid of an infection, whereas to format the machine cleanly and reinstall takes a known and finite piece of time and results in a machine that is KNOWN to be clean.
The steps are:
LOW LEVEL FORMAT THE DRIVE (to remove any boot sector Rootkits) - good time to think about putting in a brand new upgrade drive
Install the new OS (get your Windows 7 if you like)
Install your applications.
Selectively copy your data files, word docs, etc.
In the future, maintain a low privilege level account and do most of your activities as that user. Login as admin when you have to install or change some settings (or use the RUN AS function to run a program as administrator)
Use High security settings for your browser (IE) , Noscript (for Firefox) and No Javascript/Plugins for Opera (use site specific settings to allow javascript and plugs for sites you particularly trust.)