What I done so far is use a 44-pin cable connector and wired it up to a small PCB which in turn connects signals to an Arduino proto-shield via a ribbon cable. The PCB also will connect to the various voltages needed (not yet wired up).
The ribbon connector on the Arduino proto-shield will be connected to 12 of the Digital pins available on the UNO (8-for data and 4 for control). Interestingly enough, the EP-2A does not need address information. It auto advances the address based on a clock signal (one of the 4 control signals) sent from the computer (or in this case the Arduino).