Hi Aaron,
Have you seen the deployment information here:
http://www.mojoportal.com/deploymentfromwindows.aspx
The problem of broken urls sounds like you populated the db from a dev machine and want to deploy the populated db along with the web. In this situation the Menu should be correct if you are using relative urls for the friendly url mapping which is the default, i.e. ~/somepage.aspx. If you used fully qualified urls you must realize these will be different on a different server. If you mouse over the menu links you should see the url in the status bar of the browser and know whether they are correct even without clicking them.
If you populate the content system from a dev machine you can run into uincorrect urls in the content coming from the db like in Html module, Blog Forums or anything using the editor. The editor does use relative urls but if you upload images the relative path on your dev machine is usually not the same as on the server becuase on dev its usually localhost/somefolder but on production its likely a root web site. So the somefolder is part of the path entered in the content from the dev machine but is not correct on a root level production site. In this case if you change the root site on your dev machine to point to the mojoportal web folder instead of the default inetpub\wwwroot folder then you can use the url localhost instead of localhost/somefolder, this way the relative path on the dev machine will match the production environment.
Hope it helps,
Joe