Model originally uploaded to Thingiverse at https://www.thingiverse.com/thing:760093.
UPDATE 2016-03-12 - I renamed the 2nd version of the small gear, which has the larger shaft hole to "Herringbone_Gears_-Small_v2.stl" to clear things up a bit. I've also added "Herringbone_Gears-_Small_v3.stl" which tightens the hole up by about .15 mm to make a closer fit.
UPDATE 2016-03-09 - I've included a v2 SCAD file and small gear with widened shaft hole (still for dual flat shaft) that should make fitting easier.
UPDATE 2015-04-22 - I've updated this by enlarging the teeth on the large gear just a tad to prevent the gears from stalling on each other. This version is working very well for me.
I took the SCAD files and adjusted them to match dimensions from the stock, injection-molded gears that come with the R!.
If you print these, please let me know how it turns out for you and if you feel that they need to be modified. I am aiming for a drop-in replacement for the stock parts.
This is for my R1 that has a dual-flat shaft on the extruder stepper.