I think I understand what you are trying to do here. You are already paying for hosting (website) for your multi-site mojoPortal installation and you want to run a PHP application in the same hosting. If you can create Virtual Directories using your hosts' control panel, you should be able to accomplish what you want.
Using FTP (or whatever method you use to upload files to your site), create a directory inside of your website and upload your PHP application to it.
Using your hosing control panel, create a Virtual Directory and point it to the directory you uploaded your PHP app to in the first step.
Enable PHP for the virtual directory.
Open your mojoPortal user.config file and add the following line to it (add the name of the directory you created in step 1 to it before saving it to the web.config):
<add key="DisallowedVirtualFolderNames" value="NAMEOFFOLDERCREATEDINSTEP1;Admin;ClientScript;Controls;Data;FCKeditor;Modules;NeatHtml;NeatUpload;Secure;Services;Setup;SiteOffice;WebStore"/>
At this point your PHP application should be running under the virtual directory. All of your domains attached to the site in IIS will respond, for instance www.domain1.dk/phpApp, www.domain2.dk/phpApp.