Skip, there are a couple of problems with your recent posts. First off, attaching your questions to threads that have been dead for a couple of years is not as good as posting a new
thread that asks the question straight out.
Second, your question is basically "How can I create PDFs with Arabic characters that use the proper calligraphy?" (Or whatever the correct term is for your requirement.) There doesn't seem to be any XML aspect to this question, so this isn't even the right forum. Sure, you were originally trying to work with Apache FOP, but you do seem to be focusing on the core question now.
And I'm sorry, I can't answer your question. I would have assumed that using a decent Arabic font would automatically take care of ligatures and medial versus final forms and all that sort of thing, but if that isn't the case then I would suggest maybe it's a problem with Acrobat. However I have basically no expertise in the area so that's just an educated guess.
I suspect that there's not many people who do have expertise with Arabic in Acrobat, and those that do don't tend to answer questions in Java-related forums. That may seem unhelpful but it's meant to suggest you might get better answers in forums about, say, typography or Acrobat. Not that I know of any such forums. Probably Adobe itself would be your best bet for such a question.