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Here is a suggestion, for what it is worth:
Disclaimer: I co-own the Generic RA for JMS project.
To learn more about the J2EE Connector Architecture, you could have a look at Generic RA for JMS [http://genericjmsra.dev.java.net] project, try to use it in your environment and build features on top of it.
As examples of protocol adaptation and EIS connectivity, you could look at building new adapters for services available off the web. [like a Jabber/IM resource adapter]