I had the same problem as Bmarquez1997 described. The rods are not co-planar with the bottom of the gears. My work-around was different though. In Prusa Slic3r 1.41.2, I did "Object | Split", then deleted the gears, leaving only the rods. Then did a Rotate around the x-axis about 1 degree. Now, print the rods.
To print the gears, do the split, then delete the rods. Now print.
The workaround for the holders was the same as described above.
Once complete, it all fit well (the rods were slightly too long - or each had a burr...) . Either way, works great! (printed in PLA, 0.15 layer height, 0.4 nozzle, default settings, on Prusa i3 Mk3). It's Awesome! Thank you for your time designing and posting this!