Configuration of EJB timeouts in the standardjboss.xml file are described in the server configuration guide but it it not clear that these are EJB2 timeouts. There is no description of configuring EJB3 session bean or MDB timeouts.
[1] and [2] provide a starting point for this description.

[1] http://jboss.org/community/docs/DOC-9628
[2] http://www.jboss.org/jbossejb3/docs/reference/build/reference/en/html/session-bean-config.html