Well after banging my head up against a wall for several days, it looks like I figured out why the application won't run. Everythime I seemed to solve one problem, another presented itself. Well, after great labored efforts, this is how I fixed it:
I started by downloading and installing the WebProject plugin from Microsoft. The following link will give you documentation on how to use it and where to download it from. http://msdn2.microsoft.com/en-us/library/aa479568.aspx.
Once I installed it, I right clicked my website project within my DotNetNuke solution and added a web deployment project. The following are my configuration settings (right click on the new deployment project and choose property pages):
Configuration is set to Release with Generate debug information and allow precompliled site to be updated checked. The only projects I build in this configuration is the website and the deployment project.
On Outupt Assemblies I click to Mearge all outputs to a single assembly and check treat as library component.
Under deployment, I clicked Remove the App_Data folder.
Now that that is set up, I needed to modify my solution. I excluded 2 files, which aren't used in my website: admin\containers\actions.ascx and admin\skins\menu.ascx.
Next, I copied my files from my App_GlobalResoruces folder into the website bin folder.
Finally, I changed the constant pointing to the App_GlobalResources directory to point to the bin. It is in the Localization.vb file under constants (in the DotNetNuke.Library\Localization). Below I show the existing setting and what I changed it to.
'Public Const ApplicationResourceDirectory As String = "~/App_GlobalResources"Public Const ApplicationResourceDirectory As String = "~/bin"
Once I made these changes, I made sure my solution was set to debug. I built the entire solution. I then right clicked on the website and built the website. After that was done, I switched my Configuration manager to release, which is set to build just the website and the newly created web deployment project. Once that is set, I right clicked the web deployment project and build it. Once built, I copied the files in the release folder to my web server and everything worked.
From what I gathered, it was a combination of the way you build the site and the fact that the localization pointer is wrong (the pointer is set to a directory that disapears on release compile). I hope this helps someone.