Msconfig.exe is missing and other issues came up trying to remove trojans

Well, I checked related threads and don't seem to see the problems I'm having, so, here goes...
I was removing a trojan using Superantispyware and fortunately, it worked. Unfortunately, now I have other problems. What I think might have been an issue was I did check all of the boxes, but one was "Disabled Task Manager" and that seemed dubious to me to get rid of, but I went ahead and did it as per the instructions in the Read Me & Run Me thread. I'm running Windows 7 OS.
My computer rebooted, and on my admin login, on start up nothing started up besides basic windows. No messengers, no anti-virus, no tools. When trying to start any program using a shortcut it gives me the "Choose the program..." prompt and I have to manually go into Program Files, find that specific .exe to open up anything. The only things that seem to work are Internet Explorer, Word, Firefox, and a few others. Firefox asks me to Save File firefox.exe and other programs do the same once they open. SuperAntiSpyware doesn't work this way, it just loads up on my tool tray and then I can't use it, which is pretty inconvenient because this means I can't give you guys my logs at all.
Msconfig.exe when I try to run it comes up with the error that it can't be found. I looked at the other thread and it doesn't seem like that's my issue.
Also when I try to change my UAC back, it gives me the same error, file not found.
Using my Guest Login what few programs I can run, do so just fine, Firefox etc., meaning it doesn't prompt me to choose a program to go through that whole deal like with my admin login.
I didn't go through the entire Malware cleaning process, because I can't install any of the other programs now, they just ask me what program to use and I don't even know where to go from there.
Most of my programs don't work at all. Is there anything you guys can possibly think of to fix this issue? Did I somehow irrevocably cripple my computer by deleting system32 files or what? If anyone has any ideas please help me out. I have no clue what I did or what's wrong. I may just have to completely re-install Windows 7 but if possible I'd like to avoid that.