Ok, so I had some time to draw tonight, and here's what I came up with.
I'll have to machine the countershaft down to 1/4" for about an inch, but other than that it's pretty simple. The bearings are preloaded by a couple of belleville springs, and the countershaft can't pull out the pinion side because of the setscrews in the timing pulley and the fact that the pulley and both bearings are in compression between the plates due to the belleville springs.
Also noteworthy is that it's designed at 3:1 now. My original ratio was 12:60, but the smallest timing pulley with a 1/4" bore (steppers have 1/4" output shaft) were 20 tooth, so 20:60 it is!