Step 1: Forget about WebLogic for now, write a small
Java application which you can run under Java 6, and have it do the process you're now doing in WebLogic. Make sure it only uses the Java 6 version of JAXB and doesn't use any of the pre-Java-6 JAXB jars.
Step 2: When you have that working, implement the changes you had to make into the code which will run in WebLogic. Deploy that code into WebLogic, without any of the pre-Java-6 JAXB jars.