Finally figured out a workaround... Can't use the plugin's pager option and had to add some scripting.
// fill the pager
$('.boxGaleria > div').clone().appendTo('.boxNav');
// update active slide in both slideshows
var slideshows = $('.cycle-slideshow').on('cycle-update-view',function(event, opts) {
slideshows.not(this).cycle('goto', opts.currSlide);
});
// add click to the carousel/pager, correct slide index because the carousel adds a few duplicate children before and after to display correctly
$('.boxNav div').click(function(){
var index = $('.boxNav').data('cycle.API').getSlideIndex(this);
var todos = $('.boxGaleria').data('cycle.opts').slideCount;
slideshows.cycle('goto', (index-todos));
});