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Sorry for creating a new thread but I figured the new info I got from Brian was very good and could be even more useful than the other posting. Although I will still be using AppDeploy for MSI creation when this new product doesn't work.
Go to my site at http://techchucker.wordpress.com to get the new instructions. The article title is: Using EXE to MSI Converter to Create GPO Friendly Installers.
These instructions are only 1 page long!!!
Hope these can help someone.