Quick update for anyone who is trying to do the same as me.
I have now got this working the process I used is:
1) Keep all your beans packaged as before.
2) Update the ejb-jar.xml to use the latest schema.
3) Update jboss.xml to use the latest schema.
4) update the ejb-jar to have a remote reference (This is to get around the JBoss bug EJBTHREE-933 which throws a NullPointerException if no remote interfaces are provided. Once the bug is fixed this can probably be removed).
And voila it all works like a charm. We can now intercept our facade beans and all is good :)