This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
Actually, after looking at your post carefully, I have no idea what it is that you are asking. You said that the MDB deployed just fine and that the messages are moving just fine, so I wasn't quite sure what was not working for you.
Also, your post might be an instance of way too much information. The people who help on this forum are very busy (at least I know I am), and I am not about to dig through many lines of code that may of may not have anything to do with the problem. At times is is best to just state exactly what the issue is (that is, you expected one behavior and instead you got something different) and provide the minimum amount of code to illustrate the code that you think is not working correctly.
Are you asking how does a standalone client application send a message to a message queue so that the MDB can read it? If so, the answer is: pretty much the same way as an application deployed to JBoss AS would do it (which you say you already have working). The key steps are:
1) Look up the messaging server and queues via JNDI (config JNDI to look things up in JBoss AS)
2) Create a message and send it to the queue you looked up in step 1.