Power LED Shield v1.6:
http://www.chesterfamily.org/pictures?g2_itemId=10108
It not only solves the clearance problem over the USB port, but actually turned out smaller than any of my previous designs. It also has holes in the right places to match the Arduino and the connections for the LEDs are properly ordered + and -. So I'm really happy with this layout.
I'm going to proof/QA it and will send it out as soon as possible.