When i do a clean install of my OS i always install my hardware firewall first then go to MS update , after that put my software firewall, anti-virus, spyware scanner ect, then configer IE firewall ect settings, then scan, then download any other protection i need, then Morzilla firefox, scan again with online scanners, check though program files, C drive and Windows for anything supicious, then desktop procceses, then common registry places (even after hijackthis).
Then anything else i want/need.
Two things i never do are install an operating system over another one (xp oner 98SE for example) or download p2p software ect before protection.
--lee