I have all my javascript/jquery code in a file and include it into my page. Without having apache process js files as php what would be the best way to pass data from php to
Why don't you just have php render javascript directly (as JSON), then you have it available to jQuery natively.
Edit:
if you don't want to have inline js in your php page, and don't want apache to process js as php, then maybe you can src a php file which contains js.