Oh, hey! In pins_arduino.c, it says:
// ATMEL ATMEGA1280 / ARDUINO
//
// 0-7 PE0-PE7 works
// 8-13 PB0-PB5 works
// 14-21 PA0-PA7 works
// 22-29 PH0-PH7 works
// 30-35 PG5-PG0 works
// 36-43 PC7-PC0 works
// 44-51 PJ7-PJ0 works
// 52-59 PL7-PL0 works
// 60-67 PD7-PD0 works
// A0-A7 PF0-PF7
// A8-A15 PK0-PK7
That totals to 68 digital and 16 analog (84I/O), and the 128 is the same as the 256 in everything except for memory size, right? With this commented, I can basically just use these pins for I/O.
Now, the PWM timers- are they hardwired to particular ports/pins, or can they be assigned to operate on a specific pin?