I found the HOLE tool, and I am now using that for the two holes that have no electrical connection. I also fixed the problem with the via drill size, by sligtly relaxing the design rule. I also redo many of the routing wires to make them more tidy as you guys recommended. Here is an updated/cleaned version:
http://m3coupe.com/electronics/PhD/PhD- … _v10-4.png
Better? What other tips/suggestions you can throw my way?
Will