Following my comments, this should solve at least your autocomplete function. The ID is dynamically created by using the iterator you already had in your code.
$('#addRT').live('click', function() {
$('<p><label for="tags"><input id="tags'+i+'" type="text" name="relatedTags.tag.name" placeholder="Name"/></label> <a href="#" id="remRT">Remove</a></p>').appendTo(scntDiv);
$( "#tags"+i ).autocomplete({
source: availableTags
});
i++;
return false;
});