OK, if your template has a menu extension then it inevitably will load after
Acrobat. There is no easy way to get it to load before Acrobat.

You could provide the menu in an add-in and then call it from
autoopen/autonew macros in the document template, which might work (though
equally might not). You could call Acrobat only when needed, though this is
difficult to achieve on a multiple user base so if a separate toolbar would
work for you then that should not affect Acrobat.

The major problem really is that Acrobat's add-in is crap. They password
protect it so users cannot fix the code, and take a dim view of persons who
hack their software, no matter how well intentioned.