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Just to be clear: Sailfish is the firmware for the Motherboard v2.4 (or 2.5 if you happened to recently replace yours).  The Extruder Controller is a separate board with separate firmware.  As such, Sailfish itself does not modify the firmware on the Extruder Controller board. 

Sailfish requires the 3.1 Extruder Controller firmware.  There has been no later release of the EC firmware.