We are facing the similar situation we have different types of users that have their login details stored in different database etc.
We only store roles in the Jboss Portal as we dont want to move all these users into the portal database.
We have Custom login Interceptors that try to authenticated the users.
One of the outstanding issue with this is that the User Details such as email, name etc by default jboss portal will try to load from the portal Database.
I think it should be possible to populate the User Details using Custom Class something like UserIdentity i think. I haven't fully went through the code yet but this what i have so far.