According to Aeronautical Engineers, the Miami company doing the conversions, this is what they are doing to the MD
"The AEI MD
-80SF cargo conversion consists of the installation of a 85"x136" cargo door on the left side of the fuselage and modification of main deck to a Class E cargo compartment. After conversion the aircraft can carry 12 88"x108" or eight 125"x88" unit load device (ULD) or eight 125"x96" ULDs. In comparison, the 737-400SF includes 10 88"x125" pallets and a 53"x88" pallet."
They also stated that there not need to be any flight performance tests for FAA certification as the conversion would not be modifying flight systems. I can only assume this is why certification was so fast and the first example has been delivered. (first flight Sept 28, 2012, FAA certification, end of October, 2012)