Previous Malware, serious problem.

I had just recently removed some files from the registry, not realizing I didn't back them up. So now I have a serious problem with running some .exe files, such as Fire Fox, Registry, basically almost anything dealing with a .exe file will not execute, I get this error message "this program does not have a program associated with it for performing this action. Create an association in the Set Associations control panel." The files I removed I followed from a site manually showing me how to get rid of the malware, however, it turned out to be more of a hassle then what I thought it would be. Currently I can't open anything except for Safari and some folders on the computer, however, the new account I created runs fine. Is there a way I can maintain everything I have on this account and get the files running again? And if you need the site I got the manual uninstall from so you know what I deleted I can get it for you.

Thanks in advance.