Go Slow after rebuild

[Acerad]

I am after a bit of advice. I lost my motherboard and power supply after a thunderstorm (even though I had everything surge protected and on a APC UPS). Anyway, replaced the mainboard with an MSI PM8M-V (486) and replaced the power supply. PC still wouldn't boot and after testing the RAM and CPU found out that cooling fan was another problem. Replaced it and all booted up to a point. Ran a Repair with XP CD and got platform up and firing. Then installed moitherboard drivers. The machine was a bit slower and hung in some applications. Performed windows update (72 files installed). Am getting a "This version of windows is no longer secure" icon in taskbar. Previously (before crash) upgraded system from SP1 to SP2, and think now that some parts of this may be corrupt, but windows will not let me re-install from website. Have downloaded WindowsXP-KB835935-SP2-ENU for multiple installation as it appears to be the only download option. Have not installed as yet. Kept getting small screen flash up that says I have critical registry errors (?spyware) - have not seen since running ADAware. Although, ran registry check and had heeps of errors. Not game to fix - as not sure if this will cause more issues. Also got messages saying that the KB...?? (did not write down numbers sorry) security updates already installed on the machine were incorrect but windows could not locate the right ones from the system32 folder. Not sure whether to delete all KB update files from ADD/Remove and try to reinstall. Other than these computer seems 95% okay. Runs a bit slow and hangs in such things as Disk Cleanup. Also, seemed to have lost access to security centre and firewall settings in control panel! Any ideas?? Thanks