If you are migrating to JBoss, you should look at the Windup tool. It will point out all the places in your code that might require attention and give you an estimate based on how many things you will need to look at. The reports are good and categorized, and they definitely cover your use of vendor-specific code and offer tips on what needs to be converted.
http://windup.jboss.org/
There is also a maven plugin that you can add to your pom and run reports periodically when you go.
Good luck
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