I don't use the Optiboot 16 MHz tho, I always use Bobuino so Serial is at D0/D1, SPI is D10-11-12-13, and I2C is A4/A5 of D18/D19, just like on a '328 board. I like a little consistency.
The version of bootloader you use shouldn't be effected by the unique pins_arduino.h file you set up to support your Bobuino board. However the entries for the Bobuino entry in the boards.txt file do have to reflect which 1284 bootloader you use, the normal one, or the Optiboot one, as that is where the fuse definitions and top of memory size values are, and they have to match the bootloader you are going to use. It's all pretty interdependent and lots of room to get it wrong. I struggled getting my 644P chip setup correctly and even had to revert to using the bootloader and boards.txt entry for a 644P from my old version 11 Sanguino files, but it all worked out in the end. Still waiting for the 1284P chip to arrive.
Lefty