First off, great theme.
Now, my complaint :) : Why do you do the menus where you have to dig through the documentation to find the 'first' and 'second' naming convention to get them to work instead of using the proper approach provided by wordpress to assign a menu to a menu location? I'm pretty sure it's just 1 line of code you need to add to make it conform to standards.
I got it working, but was an extra hoop that is not necessary.
Anyways - just my 2cents.