malware scanners find renamed files

Hi, I recently fought off some malware on my laptop pc. One of the steps I
had to do was rename (extension) some things in the Recovery Console. My
system now seems to be fine once again.
My questions are these....What do I need to do, if anything, with the few
files that I renamed in RC? I renamed, for examp, the userinit.exe file
So far my system is running ok. The only thing that I have had issues with
is that my internet keeps 'coming and going"; meaning my broswer (IE7 or
firefox), or anything randomly loses connectivity. It happens ONLY to my
laptop. And almost daily.

Yest I did a spybot search & destroy scan and says it found coolwebsearch
and it associates itself with the winlogon.old file. Not sure but I think
that was one of the ones I renamed. Should I delete all that my
virus/spyware scanners find, even if its one of these renames? Do malware
scanners typically 'find' and consider these renames threats?
Thanks in advance
Windows XP home edition sp2