Browsers unable to connect but email ok?

I never claimed to be a rocket scientist. In effort to clean my system from spyware, trojans and hijackers I went a little too far and cleaned a little too deep. Using "Hijack This" like I knew what I was doing, I must have deleted files I should'nt have, as now I cannot connect to the internet with either IE or Firefox. Interesting though I can still get my email using Thunderbird (Mozilla). I know my network is fine as my laptop is a-ok.
When I launch IE or Firefox I get "launchmodem/redirectBS.htm" in the status line. From searches that message appears when the Bellsouth ISP network servers have issues. Again I know Bellsouth is not to blame as 2 other systems on the same network are connected fine.
Any ideas on how I can clean this mess? Is there a repair function on Win2000 CD? I'm reluctant just to try because I did'nt want to load a second copy of Win2000 and end up with a multi-boot system.

BTW - 2 days of digging for malware and the system is clean. I think I just got a little over zealous cleaning.

Thanks for any help!