We have had created several portal templates while using 4.9.1.  All (seemed to be) were succesfully created with site content.  Today, we've attempted to use those templates and resources on our dev 5.0.1 site.   

The error message;

 AssemblyVersion: 5.0.1
PortalID: 0
PortalName: My Website
UserID: 1
UserName: Super MeActiveTabID: 52
ActiveTabName: Site MeRawURL: /Admin/SiteWizard/tabid/52/Default.aspx
AbsoluteURL: /Default.aspx
AbsoluteURLReferrer: http://universal.info/Admin/SiteWizard/tabid/52/Default.aspx
UserAgent: Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; .NET CLR 2.0.50727; .NET CLR 1.1.4322; .NET CLR 3.0.04506.30; .NET CLR 3.0.04506.590; .NET CLR 3.5.20706; .NET CLR 3.0.04506.648; .NET CLR 3.5.21022; OfficeLiveConnector.1.3; OfficeLivePatch.1.3)
DefaultDataProvider: DotNetNuke.Data.SqlDataProvider, DotNetNuke.SqlDataProvider
ExceptionGUID: 676f15d7-6832-4187-8527-10f5e4205b72
InnerException: Violation of UNIQUE KEY constraint 'IX_FolderPermission'. Cannot insert duplicate key in object 'dbo.FolderPermission'. The statement has been terminated.referred to Folder permissions

Is this related to the site's template or the resources?

.. and if that doesn't work it's dirty data :).

I would open up the template files in a text editor or an or do a diffcompare with a utility.
Ultimately you might find it easier to copy the site and upgrade it.