Spent time with support and between this and google searches a resolution was found. These things need to happen:
1. Web.config needs to be changed so that <trust level="Full" /> is added in the system.web section.
2. Web.config needs to be changed so that the compilers are removed. The system.codedom needs to be empty. <system.codedom /> <!-- No compiling on server, GoDaddy blocks it. -->
3. The settings in Visual Studio for publishing the website need to be changed to enable precompiling the website.
The root cause of the issue is that GoDaddy does not allow compiling of the website on the server. This was the permission issue observed above. Once these were done the site came up fine.
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