I couldn't take all the problems and constantly fighting with my system any more. This morning I took the Nvidia card out of my Linux desktop. I plugged the second monitor into my little Windows laptop and I hooked up my main monitor to the on-board intel video.
All my issues are gone. All my software runs, the system does what it should, looks the way it should, etc. I'm not thrilled to have to work this way - synergy makes it a little more palatable but this is where I'm at for the time being. A little while down the road I'll try it again and see if things improve but for now I've got stuff to do.