You need to specify that the myrar-service.xml should be deployed by including a jboss-app.xml next to application.xml
As I recall the correct fomat is
myrar-service.xml should be in the root of the .ear
The classes in MyJCA.jar should be deployed and available to everyone without any manifest classpath references, just the application.xml reference. If this isn't happening please provide more details.
If you want to move the myjca.jar elsewhere in the .ear you will probably have to provide a manifest classpath reference to it. I don't recommend this.