Looks like you posted quite a while ago. But, I am also having the same experience. We have developed our product using JBoss and now have to port the web application over to WebSphere for the customer. At first I was going through and trying to edit the ibm-specific files myself. IBM has its own files that go in the EJB JAR, WAR, and EAR files, just as JBoss does. I have been trying to use the application development wizards and I think I'm getting somewhere, but I'm also wondering if anyone has done this before. Currently, I'm going from JBoss 2.4.4 to WebSphere 4.0 and the web application uses only stateless session EJBs and JSPs and communicates with an Oracle database.
Thankfully I have never had to do anything like this... Something you might investigate is using xdoclet. It can generate the server-specific dd's for jboss, weblogic, websphere, and I think hp and Orion (?). You'd have to do some work setting up the tags, but it might possibly be worth it. If you have to port to yet another server later it might be even more worthwhile.