Is your mojoPortal development environment installed in a virutal directory (for instance: http://mymachine/mojo)? If so, you will run into all sorts of issues and because mojoPortal builds the URLs for links, images and so forth using everything after the domain of the site, so in my example all of your links will be "/mojo/somelink.aspx".
If you are comfortable with SQL, you can make your way through the database and change any occurrence of /mojo/ to just /. I have done this in the past but I don't have my notes on which fields I had to change. My notes wouldn't be relevant anyway because it was so long ago and a lot has changed.