severe system problems windows me

despite having norton antivirus running on the system two trojan viruses infected my system.lots of programs have disappeared,also i have lost java script so functionality is poor. i cannot locate the add remove program to allow me to uninstall damaged programs then reinstall them, this includes internet explorer. when i try to install the mentioned programms they say they are installed & to remove these versions first. i have the windows disk & could reinstall but would i loose all of the varios files downloaded overtime or would it repair the windows system