Is there a way to default a queue to paused in standalone-full.xml or to maintain state after a restart?

I don't believe there is a way to do that specifically.  However...

Our problem is that MDBs start processing messages  prior to full jar deployment and that causes problems with resources not being available.

Try using the @DeliveryActive annotation on the MDB which can be set to true or false (see example here).  Then you can execute the "start-delivery" and "stop-delivery" as necessary.

One other idea is to inject your resources into your MDB and that should set up dependencies between them so that no administrative (i.e. manual) intervention is required.

In addition to what Justin noted, what specific version of JBoss AS do you use. More of a FYI - WildFly 10 has introduced this new feature WildFly 10.0.0.Beta2 Release Notes - see section named HA Singleton MDBs and MDB Delivery Groups (the delivery groups is what is relevant to this discussion).