Sorry to answer so later, its been a looong day. For that board and layout you should be more than fine downloading the Leonardo bootloader. If you use the Arduino IDE it will write the fuses for you.
Let me know if it worked.
@Nick - I recomend the AVR ISP MkII from Atmel and any old Arduino should do the trick too. The moded AVR ISP mkIi is the one I use to flash the Leonardo bootloader to all the vinciDuinos. If you order from Digikey as part of something else you save on shipping costs.