Hi Killer,
Glad you got everything working again. Now, with a new Win 7 installation, there shouldn't be "essentially anything" to clean up. Great!
As you listen to top pros discuss registry cleaners, Fred Langa for instance likes CCleaner, and jv16 PowerTools.
CCleaner is free, and can be very helpful, or thorough, rarely harmful. You have to choose the features you want and just use those.
CCleaner has a nice feature I use almost daily, which cleans out the Tracking Cookies, and Temporary Internet Files, Temp files and does no harm. It has a list for "important cookies" you choose that don't get deleted, say with your Amazon or Citibank account numbers.
It also has a section with choices, that scan and show orphan or bad registry entries. That section also saves the registry changes in "My Documents" so if you inadvertantly remove a needed entry, you can just click on the saved .reg file and it is placed back in the registry.
But you have to be careful not to remove, say a .Net Framework 2 entry that one of your programs use.
I use that to clean out unused file extensions, and after uninstalling a program, the programs left over registry entry items. But leave the CLSID and Uninstallers, Fonts alone.
the jv 16 power tools he likes also, but it is more sophsitocated, and you have to understand what each section does or it (you) could cause trouble.
The one lesson about Registry cleaners I've learned over the years is that if you delete an item you don't understand just for thoroughness, one of your programs you might not use for a couple weeks becomes useless or unstable, and you can't associate one with the other.
The good news is you now have a clean. malware free, and happy Windows 7 Installation that should be great.