I am not aware of an automated process that can achieve what you want. One way to do this would be to write a startup class that will bind these key/value pairs for you when the server starts. If you are paying for a weblogic license, you should email support. That might shed some light into the problem. If you do find a way to do this declaratively, do let us know.
At the end, the solution I came from reading these posts/articles is to deploy an ear containing the properties files as a shared library and
then use the ClassLoader to load the files into my modules.
Since your did indeed use shared libraries, perhaps you could have loaded the properties files into the JNDI directly instead of accessing the class files in the other application using the ClassLoader. Just a suggestion
subject: WebLogic 10.3: how to add System Property/new global JNDI object at server startup