You did not mention:
- What version you upgraded from?
- What version of .NET 3.5 or 4?
- Which database platform?
What do you mean "copied back the Web.config"? You should use the Web.config file that shipped with mojoPortal and restore any customizations such as machine key from your old one to the new one.
If you are seeing default content instead of your site content, it sounds like your database connection string has changed to a new database, check your connection string in user.config and make sure it is correct.
Hope that helps,
Joe