You said you have gotten it to work... do you have search friendly URLs turned on?
I ask, because it seems that if I turn them off, alternate ports start working.
I've currently configured my dev site on port 8088 in IIS, manualy added the :8088 to my HTTPAlias values in the PortalAlias table, and have the UserPortNumber set to true (and uncommented) in web.config.
This is the ONLY way I've been able to get alternate port numbers to work.
When Friendly URLs are turned on, it attempts to go to the correct URL, e.g. http://localhost:8088/Login.aspx, but I just get the 404.
Maybe there is something else that needs to be configured for friendly URLs? I'm new to DNN, so maybe this will ring a bell with someone else.
--Eric