Couple comments -
Missing INT2 on PB2
Arduino pinout- can you add the alternate Bobuino Pinout? I think its more useful
// ATMEL ATMEGA1284P on Bobuino
//
// +---\/---+
// (D 4) PB0 1 | | 40 PA0 (D 21) AI 7
// (D 5) PB1 2 | | 39 PA1 (D 20) AI 6
// INT2 (D 6) PB2 3 | | 38 PA2 (D 19) AI 5
// PWM (D 7) PB3 4 | | 37 PA3 (D 18) AI 4
// PWM/SS (D 10) PB4 5 | | 36 PA4 (D 17) AI 3
// MOSI (D 11) PB5 6 | | 35 PA5 (D 16) AI 2
// PWM/MISO (D 12) PB6 7 | | 34 PA6 (D 15) AI 1
// PWM/SCK (D 13) PB7 8 | | 33 PA7 (D 14) AI 0
// RST 9 | | 32 AREF
// VCC 10 | | 31 GND
// GND 11 | | 30 AVCC
// XTAL2 12 | | 29 PC7 (D 29)
// XTAL1 13 | | 28 PC6 (D 28)
// RX0 (D 0) PD0 14 | | 27 PC5 (D 27) TDI
// TX0 (D 1) PD1 15 | | 26 PC4 (D 26) TDO
// INT0 RX1 (D 2) PD2 16 | | 25 PC3 (D 25) TMS
// INT1 TX1 (D 3) PD3 17 | | 24 PC2 (D 24) TCK
// PWM (D 30) PD4 18 | | 23 PC1 (D 23) SDA
// PWM (D 8) PD5 19 | | 22 PC0 (D 22) SCL
// PWM (D 9) PD6 20 | | 21 PD7 (D 31) PWM
// +--------+
//