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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).

Direct (non-bowden) extruder for Ultimaker