Actually it's unlikely that its a module issue. Some of the factories are registered via a callback from the jsf impl. If for some reason a faces-config is not processed this could happen. I added some additional logging for when the factories are registered. If you could try this binary instead:
https://repository.jboss.org/nexus/service/local/repositories/snapshots/content/org/jboss/spec/javax/faces/jboss-jsf-api_2.0_spec/1.0.1.Alpha1-SNAPSHOT/jboss-jsf-api_2.0_spec-1.0.1.Alpha1-20110808.223924-2.jar
It now will log when the faces context factory (and others) is registered:
17:36:39,508 INFO [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-8) Initializing Mojarra 2.0.4 (FCS b09-jbossorg-4) for context '/jsf-injection'
17:36:40,303 INFO [javax.faces] (MSC service thread 1-8) Registering factory: javax.faces.application.ApplicationFactory impl com.sun.faces.application.ApplicationFactoryImpl
17:36:40,304 INFO [javax.faces] (MSC service thread 1-8) Registering factory: javax.faces.context.ExceptionHandlerFactory impl com.sun.faces.context.ExceptionHandlerFactoryImpl
17:36:40,305 INFO [javax.faces] (MSC service thread 1-8) Registering factory: javax.faces.component.visit.VisitContextFactory impl com.sun.faces.component.visit.VisitContextFactoryImpl
17:36:40,305 INFO [javax.faces] (MSC service thread 1-8) Registering factory: javax.faces.context.FacesContextFactory impl com.sun.faces.context.FacesContextFactoryImpl
This is supposed to happen *before* the faces servlet is initialized.