If you have the cable, then plug it into your PC's parallel port and the ICSP header for the Atmega on your MD board. Also plug in the board via USB. Then, using ponyprog, choose your device (avr micro -> atmega32), choose parallel port in 'setup -> interface setup', set the configuration and security bits using the attached file as a guide ('command -> security and configuration bits'), load the firmware .hex file and then burn it to the chip with 'command -> erase' and 'command -> write all'. You should now have the firmware loaded. I haven't done this operation in over 10 years so might have forgotten something, but I think it should work.
fuses32.png
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If it ain't broken... fix it until it is.