Windows XP Cleanup and MGtools

After completing the entire Malware removal process as provided, all the way through the Windows XP Cleanup process, I have used the Control Panel to "uninstall" each of the downloaded tools. Since ComboFix and MGtools never appeared in the Control Panel as loaded programs, can I just delete ComboxFix and the MGtools directory without leaving stray elements behind - particularly in the registry?

My objective was to cleanup my system to the extent possible without actually wiping the entire disk and having to reload the OS. No Malware or other real problems were identified anywhere along the way so I am now just trying to make sure I keep the system as clean as possible. A slow boot-up and slow response in opening files convinced me that a general cleanup was necessary. This drifts from a Malware subject to a degree but I would like to get the registry as clean as possible in the process. Do you have a particular recommendation (that is free) for cleaning the registry that would do any better than the registry cleaner within CCleaner?

One other note, perhaps for the benefit of others, in searching the forum for an answer to my original question I found a thread dated 3-23-10 at 2:15 pm initiated by Poppi22 titled Problems with MGtools. The initial comment was that when MGtools was executed a window opened very, very briefly and there was no log created. I encountered the same thing. After some head scratching I decided that since I hadn't been asked to reboot at anytime during the Malware removal and cleanup process I should do so. I also had turned off the automatic startup of SuperAntiSpyware before the reboot. I have no idea whether the reboot by itself changed something or whether the absence of SuperAntiSpyware had an effect, but the point is that after the reboot I ran MGtools and it worked as it should have. No particular need to respond to me on this unless you have a short explanation off the top of your head that you chose to offer.

Thank you for any assistance you have to offer.