Windows XP Pro hangs during startup after virus cleansing

hi! thank you for accepting my membership application... it was fast.. anyway i need to find the best approach of restoring my friend's windows xp professional... after using spybot search and destroy and finding almost 100 virus, spywares, malwares, trojans, it only allow me to log in my password... can't decide what to do, whether by using the cd installer or by performing repair install... i am worried that the accounting and inventory program for their pharmacy outlet will be affected... what is the best thing to do? thanks in advance..

lmtorres