After spending two hours fucking with pushing my reset-button and clicking upload in both ReplicatorG and Makerware, I figured out how to do it from the command line. The command line was determined from running ReplicatorG on the console and trying to upgrade the firmware.
Download and install it from http://www.makerbot.com/sailfish/install/
wget http://firmware.makerbot.com/firmware/MB-mb24-2560-Sailfish-v4.4-r1029.hex