1. Align the header with 2.54mm grid. Related discussions: http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1206626508 Place an second row of header align to standard grid. So it will be compatible to existing shield and your proto board. Both of the headers will be soldered, or either of them.
3. Possibility for USB HID support.
Is it possible to do ? What solution do you have ? Headers with a 1.27mm pitchs ?