First of All remember that you are using too many of JS files. And wordpress also has different plugins. You have to use jQuery.noConflict() The documentation is here. https://api.jquery.com/jQuery.noConflict/
I was not able to find this anywhere in your page. Anything with class "story" was not present.
$(".contentsection.story").offset();
This line was causing errors and breaks in js.
You have prevent default being called to those anchors. by this function.
$('#nav a, .arrow a, .anchor, .featurecaption .button').click(function(event){
event.preventDefault();
$('html, body').stop().animate({
scrollTop: $( $(this).attr('href') ).offset().top - 100
}, 1000, "easeInOutCirc");
return false;
});
Now this is being called and hence your anchor tags dont work and scroll. Also the line. $( $(this).attr('href') ).offset().top is bit of confusing for me. Try to jQuery.noConflict() before writing your costume functions.