Ok, first off "somewhere in the process" is probably going to scare away most people that could help you out here considering the symptoms you are having. Please ellaborate on what you did to remove the software from your computer. You did the right thing in removing the scanner software. I'd remove it all completely including disconnecting the scanner and remove all software relating to the scanner until your computer boots properly.
secondly, what is happening with your computer when you try to restart it?