I have MojoPortal installed under inetpub/wwwroot/mojortal
I change the default IIS website to home directory inetpub/wwwroot/mojortal
I don't understand, if the sites were already working it sounds like you already have it pointing to inetpub/wwwroot/mojortal
or maybe you have a copy of the files both in the wwwroot folder and in the mojoportal folder and that is causing a problem?
in any case one thing you need to know is the version of mojoPortal in the Web App Gallery is not the latest version and it is for 3.5 .NET not 4.0.
you should download from codeplex and upgrade to the latest 3.5 version then download the latest 4.0 version if you want to change to 4.0 .NET
and of the downloads can be installed similar to the way it is installed from the gallery