Scott, your link was for Spybot. I have 1.2 but 1.3 is now available. I updated to 1.3 and it did find more. I believe 122 problems. I checked the startup manager and all the .exe files are still there. But it is down to 75 files now. I didn't delete 31 from the registry do I guess Spybot might have done a few?
Anyways thanks for the help so far and if you have anymore suggestions on what I could do next it is greatly appreciated.
Despite what JFE says you are alright.