Print the parts. There are two driveshafts, for motors with 20 and 24 mm shafts, others can be produced from the .scad file. Also, there are two versions of the main body, one with "fixed2" in the name (the original) and the other, marked "fixed4", where a couple of minor manifold issues have been fixed with netfabb. These should otherwise be 100% identical and the netfabb-fixed one should slice and print more reliably, but I have not actually printed that one.
I recommend 0.20mm layer height. 0.25 might work too, but more than that probably won't. Note: PLA is sort of food-safe, but ABS most likely isn't. Don't use ABS except when printing for purely decorative purposes.
Drill a hole in the nozzle, 1.2 mm and 1.6 mm are good starting points. Cut a gasket for the nozzle flange, I used bicycle inner tube. Attach nozzle with M3 nuts and M3x10 bolts.
From the other end, push the rotor all the way into the stator cavity, then fit the driveshaft and attach a NEMA17 stepper motor with the motor coupler piece fitted to the end of the motor shaft (requires flats on two sides), making sure that the coupling teeth fit together.
The extruder should now be ready to be fitted to the printer - it bolts directly into the latest Prusa X carriage with the 40mm circular hole.
The extruder also needs warm air - otherwise trying to get repeatable results or results at all is hopeless. The pipe opposite the funnel can be used to fit an air hose (I used a washing machine water outlet hose). The air circulates inside the heat shroud around the pump and inlet block and exits around the funnel. A shoe dryer supplies the warm air in my setup. The temperature should be just a little below 30C.
The object to be printed can be sliced into GCODE pretty much the same as when printing with plastic, but the layer height should be larger to accommodate the larger nozzle, and the filament diameter has to be set much higher. In my setup, with E_STEPS_PER_MM set in the firmware to 1800 and with a 1.2 nozzle, I used 18mm as the filament diameter to print the Flying Spaghetti Monster seen in the pictures. (Layer height was 0.7mm). The effective filament diameter also depends on the nozzle size, since smaller nozzles cause more backflow in the pump (because with plastic parts, it won't seal properly). Also, set the infill density to 100% - chocolate really doesn't handle overhangs...
Then it's time to melt some chocolate (I wrote a bit about it here: http://reprap.org/wiki/Chocolate_Extrusion but the main point is: don't exceed 33.8C), pour it into the extruder's supply funnel and see what happens.