Don't update the firmware to change the steps. Instead you can enter the gcode command M92 E(number of steps). Once you have the right steps/mm dialed in, you can store it in the electronics by entering M500 or in Repetier going to Config - Configure EEPROM Settings.
Slic3r and the newest Skeinforge versions calculate the flow rate automatically, but the extruder needs to be calibrated to carry out those calculations correctly. Adjustments can be made in the slicer settings, but it is still best to use a calibrated extruder as a starting point.
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