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This is a list of the ATMega pins that are used for various ad-hoc I/O on the FC.
The A/D converter inputs, the ISP interface, I2C and the air pressure circuit and 
red and green LED outputs are not included.

ATMEGA pin      FC1.3 name    FC 2.0 name       Used for
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PC7             SPEAKER       SPEAKER           Beeper.
PC6             J6            SERVO_R           FC1.3: J9. FC2.0: Reset on IC5/4017.
PC5             PC5           PC5               Expansion port pin 6. "SPI slave select" in spi.c.
PC4             PC4           PC4               Expansion port pin 5. PWM in from MK3Mag compass.
PC3             PC3           PC3               SV2 pin 1 via transistor. Also known as J17.
PC2             PC2           PC2               SV2 pin 5 via transistor. Also known as J16.

PD7             SERVO         SERVO_C           FC1.3: J7. FC2.0: Clock on IC5/4017.
PD6             ICP(PPM)      ICP(PPM)          R/C PPM signal in.
PD5             J3            J3                R/C channel 5 forward (rc.c). Auto-zero feature on InvenSense gyros (InvenSense.c, dongfang only).
PD4             J4            J4                R/C channel 6 forward (rc.c). Execution time measurement of main loop (main.c).
PD3             J5            J5                TXD1 with ATMega644p. R/C channel 7 forward with ATMega644.
PD2                                             RXD1 with ATMega644p

TDX1 and RXD1 are the 2nd UART in ATMEGA644p. It can be used for direct connection of a UBlox GPS module (no Navi-Ctrl), or for connection of a Spectrum or DSL serial R/C satellite.