I just squashed a bug that was preventing me from styling the icons in Menu 1.
The issue is that I have my blog set up to use the http://site.com/?cat=1 style of URL. When your bfa_simplify_wp_nav_menu() function ran, it created class names of cat-?cat=1, which is not valid CSS and could not be matched (at least in Chrome).
Small-scale solution is to add the following line right before adding slugs to new_classes (line 175):
Code:
$slug = str_replace (array('=', '?'), '', $slug);
Best part is that fixing the issue there makes the generated code on the "Using Menu Icons" admin page generate properly.
In any event, thanks for the great theme and I look forward to further unpacking it.