Hi Bill,
AIJ was not originally intended as a scriptable tool, but AIJ user GeorgeF has found a very creative way through the use of ImageJ macros to access AIJ functionality using the preference settings that AIJ uses to store and recall all settings between AIJ sessions. I unfortunately don't have time right now to support your effort directly, but I would encourage you to review the documentation and examples on this post by user GeorgeF:
http://astroimagej.1065399.n5.nabble.com/Running-AstroImageJ-Data-Processor-in-Batch-Mode-td1257.htmlPerhaps if you are close to a solution and have some small questions about George's approach, a brief description of your question in the above post could possibly result in a response by George, if he has time.
Karen