I recently had a few problems with the JBoss 3.2.2 transition as I made the foolish choice of starting to use XDoclet as well. The original jboss.xml and ejb-jar.xml hand-built deployment descriptors had a few failures under the new release so I thought I might as well transition things over to get the pain over in one hit. At least in theory it should allow future transitions to be easily and automatically made by recompilation.
I hit a problem in that XDoclet 1.2b4 did not support the jboss.xml element ejb-local-ref, necessary for accessing other EJBs by their local interface where these EJBs were in another application space. I also noticed after implementing the changes that the JBoss DTDs in the current XDoclet bundle are a bit outdated compared to JBoss 3.2.2 DTDs and don't declare the ejb-local-ref element. So I've provided a walkthrough on fixing the problem until the XDoclet team update their builds. You can get the PDF from http://www.amitysolutions.com.au/documents/XDocletChange-technote.pdf. It should also give you an idea of how to make changes for any other customizations you might require.
Hope this is of use although it might be quick and dirty. I'll eventually get around to writing a JBoss-centric guide to XDoclet use, and the indirection between ejb-jar.xml and jboss.xml for newbies as this seems to get the most questions (or causes the most confusion) in the forums. However, I've got a few other things on the plate at present.