Well it should be that simple. The 1280 bootloader hex file is located it the Arduino core folder called
ATmegaBOOT_168_atmega1280.hex . And the fuse settings are located in the 1280 section of the boards.txt file also in the arduino core directory.
##############################################################
mega.name=Arduino Mega (ATmega1280)
mega.upload.protocol=stk500
mega.upload.maximum_size=126976
mega.upload.speed=57600
mega.bootloader.low_fuses=0xFF
mega.bootloader.high_fuses=0xDA
mega.bootloader.extended_fuses=0xF5
mega.bootloader.path=atmega
mega.bootloader.file=ATmegaBOOT_168_atmega1280.hex
mega.bootloader.unlock_bits=0x3F
mega.bootloader.lock_bits=0x0F
mega.build.mcu=atmega1280
mega.build.f_cpu=16000000L
mega.build.core=arduino
##############################################################
Only complication would be if your boards are not running with an external 16mhz crystal or resonator, that would require changes to the bootloader hex file (baudrate value) and the boards.txt file.
Not sure what software tools you would use with your programmer, but If it can read and burn the hex file and can set fuse bits, it should be straight forward task.
Lefty