Forcing the Intersecting geometry is helping. I should have made the model cleaner and saved myself a lot of work. I am used to using a Boolean operation and just discarding the extra geometry. I have to admit, Sketchup is a quick way to give ideas shape. It has some issues with rounded surfaces though.
Maybe I should try a Follow Me and see if I can get the glass to fill in the way I want it too. Thats a nice lofting tool but it seems to jump around a lot on me while trying to pick the path.