Summary

In the beginning there was Three Cube Gears by emmett. Then came Geared Cube, Hand Crank Edition by gzumwalt.
This is more rugged version of gzumwalt's model.
Designed in MOI, printed in Diamond Age PLA on an Ultimaker 1.
A short video is here: http://youtu.be/quQQPeJRWsE

Important Note. To make this you need to make all of Three Cube Gears by emmett excepting only one of the large corner pieces and the central hub.

Instructions

Notes.
The shaft is slightly larger in diameter to accommodate the pinion and the handle. This eases assembly.
The holes in the box should be cleaned/opened so the the shaft can rotate freely. The pinion (especially) should be a light press fit on the shaft. To assemble the pinion start the smaller end of the shaft into the box and into the pinion and then push the shaft towards the far end of the box, then fit the 'tool' around the shaft so that it fits between the pinion and the far side of the box. Then press or tap the shaft home.
I made the bolt at 100% fill, all else with 1.2mm walls and 20% fill.
Note that the threads on the bolt are non-standard. For those interested I've doubled the standard (coarse) ISO pitch and increased the included angle from 60 degrees to 90 degrees.
I opted for separate nuts rather than threaded holes in the box so that it is trivial to adjust the fit of the nuts to the bolts. If too loose or too tight scale the X and Y axes in your slicer. (Not the Z axis as that would affect the pitch of the thread.)

Geared Gear Cube - a more rugged version of Geared Cube, Hand Crank Edition.