Makerbot and reprap machines have different firmware settings because the mechanical hardware is different.
Are you running a typical Gen3 setup? (3 stepper drives, 1 reprap/sanguino mother board, 1 extruder board)
Info you need to have in order to make software adjustments
-Stepper motor info: 1.8o/step or 0.9o/step (look for a sticker on the motor)
-Pulley info: how many teeth
-Temperature sensor info: You need to know the specs of sensor you are using to read temperature.
-extruder type: to determine a starting point for the extruder stepper setting
-Decide if you are going to use the reprap host or SFACT to generate GCODE
hope this helps
Dan