We did an upgrade of IM r12.6.4 to IM r12.6.8 and upgraded JBoss from 6.3 to 6.4 at the same time. So similar to your requirement.
I installed the new Identity Manager software onto the new version of JBoss and pointed it at my existing IM Object Store database server. As I had previously split out the databases, I then updated the standalone-full(-ha).xml file so that the other data sources pointed at their directories. If using a JBoss cluster, there may be some other updates to this file that were made during the previous IM install, so they need to be made here again.
If you're sending email, you'll need to re-enter the SMTP server in standalone-full(-ha).xml and re-enter the sender's "from" email address in "email.properties"
Other than that, you would need to copy across any UI customizations you might have made (e.g. replace logo) or any custom code you've developed and deployed. If you had configured SSL on JBoss, that needs to be re-configured.
And if you're using Workpoint Designer, you will need to follow the documentation instructions again and edit init.bat and WorkpointClient.properties, as well as copying across the correct JAR files