There's an example of looking up an EJB 3.0 bean via JNDI from a servlet 2.4 module in the InfoCenter. Basically, setting up the ejb-ref in your web.xml is similar to if you were pointing at an EJB 2.1 bean, except since EJB 3.0 beans don't have homes you put nothing in for the home entry in the ejb-ref. (But I definitely recommend you look at the example.)
For question 2, you may want to check out the EJB 3.0 feature pack InfoCenter documentation. If your client is a Web container, EJB container, or application client container that has the EJB 3.0 feature pack applied, you don't need to generate the stub classes with createEJBStubs.bat (assuming that your WAR module at least includes the .class file for the EJB remote business interface, the stub will be generated in-memory by the container you're calling from).
As you mentioned, @EJB injection is supported in servlets. Since your servlet is not in the same application as the called EJB, WebSphere's auto-link feature doesn't apply and you need to resolve the linkage between your @EJB injection and the target EJB using entries in the WebSphere binding file in the WAR module.