Yes, using the Bowden extruder design for printing Ninjaflex seems to me quite hard, (if possible at all). Perhaps you can give it a try with a non-bowden design like: http://www.thingiverse.com/thing:310095
My Ninjaflex order should arrive soon. Very likely I also have to make some modifications to my Greg/Wade extruder before it will start printing rubber properly. But my changes should be minor (like extending the filament guide with some PTFE tube).