Replace your javascript with this

$(document).ready(function(){
	$("a[rel^='prettyPhoto']").prettyPhoto({
			// Only add stuff that you really need :-)
		});
});

Excellent!!! Thanks so much - you are a miracle worker!

Let me ask you another question: if I just leave the java in the header with no variables, can I then put java in each post with variables and have it override the header?

I don't think so. Just add the vars that you really need to change, also don't use \ at line breaks as you did before.