Lots of malware removed, but I think something remains

In running the malware remove procedure I ran MGtools and got a missing .dll error since I did not have .NET, so I installed SP3 for XP and .NET 1.1 and 2.0 and reran. I noticed that in the second run, MGtools removed files before running the newly installed .dll this leads me to believe (right or wrong) that something has not been caught, and it is repopulating my system with malware. MGlogs-1.zip are the logs from the 1st run of MGtools.

 

Here are the MGtools logs.

 

The main problem has been extremly long hard drive scans at start up, and then at random times there after. The start up hard drive scan is taking less time now (In addition to removing the malware, I have also disabled file indexing). The drive is currently doing a couple of short scans each minute, regardless of if the system is doing something or not.

 

I recently defragmented, used the startup manager in ccleaner to disable all but the most important items at startup (also disabled the alternative user input service per microsoft knowlegebase, so I no longer have ctfmon.exe at startup or acting as a resource hog--The Regsvr32.exe /u msimtf.dll command failed to unload msimtf.dll but the Msctf.dll unloaded without a problem), and ran CHKDSK which found no problems (It said the disk was clean, I had check the auto fix option). Even with the system tray items shut down I still get the short hard drive reads.

 

Okay, thanks. The only Malware issue I was having was the long startup time which has been resolved with the cleaning.