1. When you create portal by UI "Add New Portal" button, you created a portal with full features as sharelayout, navigation, skin... But it's not a web application (it's a component that managed by GateIn), so there is no war file. If you are tired with guide http://community.jboss.org/wiki/Createanewportalcontainerusingextension, you can edit example of GateIn here: https://anonsvn.jboss.org/repos/gatein/portal/trunk/examples/extension/. It's easy.
2. AFAIK, There is no eclipse plugin for creating portals or portal containers
3. Maybe, you forgot to change name of some folder that containers stylesheet files