I just pushed it the new clickonce version with the update, and it was marked as 2.0 in the file so I kept it as 2.0. Whoops!
FYI:
Reading the fix for the startup I don't think that will work. The reason is the path to ClickOnce apps are always changing. Thus, if the app is clickonce deployed we have to go a different route. Not hard.
All that needs to be done is we write a shortcut URL with the URL of the application.
-Keith