With the help of the guys over at xs11.com, I figured out that a tiny dowel was missing that would not let me shift into fifth gear. Not sure what happened to it, but it is gone and a new one has been ordered.
Now I am working on the clutch lever, which is very hard to pull.
After the parts arrive I will reclean the carbs and start the bike up.
Ok, I am having some trouble with the shifter. Sometimes it will slip right into gear, other times the shifter goes limp and other times it locks up for a moment. I thought it could be the tension spring but that looks good. Here is a video of the shifter and gears in action. Any thoughts would be appreciated.