The bootloader needs to be flashed using an ICSP programmer. The easiest way to do that is to use the Arduino IDE, which has a burn bootloader option. The actual bootloader binary lives in the arduino core directory and is referenced by boards.txt.
As for the 16u2 firmware (it's not really a bootloader, just a program that runs in the 16u2), the source is at https://github.com/Pinoccio/hardware-pinoccio/tree/master/firmware/atmega16u2/lufa-100807. I'm not exactly sure if the compiled .hex file is online somewhere, though. @eric, do you know? If not, could you look up the .hex file used in production and send it over so I can publish it?