Hi,
Have you checked the mojoPortal System Log for errors?
If you delete all of your existing site files, none of your existing uploaded content files will be available to the site. For instance, if you uploaded graphics and flash files for use in content, you will lose those and need to upload them again.
When you upgrade, you should never keep your existing web.config file. If you have made changes to your web.config, make note of those changes and then make them in the new web.config file one at a time.
My suggestion is to take a look at the System Log and fix any problems that you see. We can help with specific problems.
HTH,
Joe D.