The code is divided by processor. The first section...
#if defined(__AVR_ATmega1280__) || defined(__AVR_ATmega2560__)
...
#elif ...
...is for the ATmega1280 and ATmega2560 processors. Find the section for your processor. If your processor is not listed, the last section is used...
#else
...
#endif
Within each section is a definition for tone_pin_to_timer_PGM like this one...
const uint8_t PROGMEM tone_pin_to_timer_PGM[] = { 3 /*, 1 */ };
Change the number to the timer you want used for tone. Using the line above as an example, the following moves tone from timer 3 to timer 2...
const uint8_t PROGMEM tone_pin_to_timer_PGM[] = { 2 /*, 1 */ };