Look at boards.txt to see where the bootloader is:
Then look in hardware/bootloaders/atmega. You'll find the source file ATmegaBOOT_168.c and the make file Makefile.
In Makefile you will find:
mega: TARGET = atmega1280
mega: MCU_TARGET = atmega1280
mega: CFLAGS += '-DMAX_TIME_COUNT=F_CPU>>4' '-DNUM_LED_FLASHES=0' -DBAUD_RATE=57600
mega: AVR_FREQ = 16000000L
mega: LDSECTION = --section-start=.text=0x1F000
mega_isp: TARGET = atmega1280
mega_isp: MCU_TARGET = atmega1280
mega_isp: HFUSE = DA
mega_isp: LFUSE = FF
mega_isp: EFUSE = F5
Change AVR_FREQ and re-build.
NOTE: Only the values 16000000 and 8000000 are supported by the Arduino core. If you use any other values the timing functions (millis(), delay(), micros(), and delayMicroseconds()) will not be accurate... and different functions will be off by different amounts.