I just compiled the unmodified STK500V2 bootloader and got a similar size discrepancy. You need to understand that the original .hex file was compiled many years ago using a much older version of avr-gcc. It's not surprising there is some difference. I flashed the newly compiled bootloader to my Arduino Mega 2560 and I am able to upload with no problem. So I suspect the problem is related to your modifications. Try compiling the unmodified bootloader source and flash it to your board to see whether you can upload with that bootloader.