1. Go to c:\arduino-1.0.

3\hardware\arduino\bootloaders\, make a copy of atmega folder, I name my

new folder atmegad2
2. Inside atmegad2, edit ATmegaBOOT_168.c, look for the main() function and add the following
uint16_t w;
#ifdef CLKDIV2
// Disable interrupts
ch = SREG;
cli();
// Enable clock change
CLKPR = _BV(CLKPCE);
// Change clock division
CLKPR = 0x1;
// Enough time for new clock to be stable?
asm volatile(
"nop \n\t"
"nop \n\t"
"nop \n\t"
"nop \n\t"
);
SREG = ch;
#endif
#ifdef WATCHDOG_MODS
...

3. Edit Makefile, add a new build target (I added right below atmega328_pro8_isp: isp)
atmega328_pro16div2: TARGET = atmega328_pro_16MHz_Div2
atmega328_pro16div2: MCU_TARGET = atmega328p
atmega328_pro16div2: CFLAGS += '-DMAX_TIME_COUNT=F_CPU>>4' '-DNUM_LED_FLASHES=1' -DBAU
D_RATE=57600 -DDOUBLE_SPEED -DCLKDIV2
atmega328_pro16div2: AVR_FREQ = 8000000L
atmega328_pro16div2: LDSECTION = --section-start=.text=0x7800
atmega328_pro16div2: $(PROGRAM)_atmega328_pro_16MHzDiv2.hex

4. Create a batch file env.bat, content below. This is to set correct building environment for the boot
loader. You do not need a separate installation of WinAVR as the current version of WinAVR has some
definition problem with Arduino bootloader source. The WinAVR within Arduino distribution is just fine.
set path=c:\arduino-1.0.3\hardware\tools\avr\bin;c:\Apps\arduino-1.0.3\hardware\tools\avr\utils\bin;%PAT
H%

5. Open a command prompt, cd into c:\arduino-1.0.3\hardware\arduino\bootloaders\atmegad2\, execute

the follow:
c:\arduino-1.0.3\hardware\arduino\bootloaders\atmegad2>env.bat
........
c:\arduino-1.0.3\hardware\arduino\bootloaders\atmegad2>make atmega328_pro16div2
avr-gcc -g -Wall -O2 -mmcu=atmega328p -DF_CPU=8000000L '-DMAX_TIME_COUNT=F_CPU>>4' '-DNU
M_LED_FLASHES=1' -DBAUD_RATE=57600 -DDOUBLE_SPEED -DCLKDIV2 -c -o ATmegaBOOT_168.o A
TmegaBOOT_168.c

avr-gcc -g -Wall -O2 -mmcu=atmega328p -DF_CPU=8000000L '-DMAX_TIME_COUNT=F_CPU>>4' '-DNU

M_LED_FLASHES=1' -DBAUD_RATE=57600 -DDOUBLE_SPEED -DCLKDIV2 -Wl,--section-start=.text=0x7
800 -o ATmegaBOOT_168_atmega328_pro_16MHzDiv2.elf ATmegaBOOT_168.o
avr-objcopy -j .text -j .data -O ihex ATmegaBOOT_168_atmega328_pro_16MHzDiv2.elf ATmegaBOOT_168_at
mega328_pro_16MHzDiv2.hex
rm ATmegaBOOT_168_atmega328_pro_16MHzDiv2.elf ATmegaBOOT_168.o
c:\arduino-1.0.3\hardware\arduino\bootloaders\atmegad2>

When the building ended, you should have ATmegaBOOT_168_atmega328_pro_16MHzDiv2.hex in the

folder.
6. Use you ISP programmer, burnATmegaBOOT_168_atmega328_pro_16MHzDiv2.hex into
ATmega328p chip. You do not need to reprogram the fuses but just in case you need, the fuse settings are:
HFUSE = DA
LFUSE = FF
EFUSE = 05