I just want to clarify something here, you say you've uninstalled IE from your computer but it still keeps popping up? Even by Windows usual standards that's quite an achievement.
As for regedit, I've modified it successfully few times successfully but that was only ever very small changes. It's a very complicated program and can cause a lot of problems/wierdness if it is messed up. Using it to remove IE sounds like a bad idea on general principles. The other problem is that I'm not entirely sure the the Internet Explorer and the Windows Explorer are two separate programs. The Windows Explorer also has a long list of obscure and little-known command-line options showing that it's more than a simple file browser so I wouldn't go uninstalling that.
One idea you might try, just to see if it works, is, when the pop-up appears again, don't bother closing it or minimizing it. Instead re-size it to be as small as you can get it, push it out of the way somewhere on the edge of the screen and carry on. That way, hopefully, when another ad appears, or whatever it is, it will appear in the same window which will not be a problem anymore. Inelegant, I know, but worth trying as a temporary fix.