Measure you your distance VERY carefully. For a small drill hole you should always use a center punch so the drill head has something to sit in before you start drilling. How big are your gears and what do you think is a good tolerance for placement?
I was just thinking about that too. Especially how to fix the ball bearings into the slots. We should both take a closer look at the website with the picture of that gearbox.
EDIT, oh, if you look carefully you might notice that on the picture of the gearbox I sent, it only has one driven gear and one driving gear (oinion). The driven gear fits into a regular hole with ball bearings, but the pinion passes through a large slot much bigger than itself. The motor screws are mounted to slots that let the motor slide back and forth to adjust the gear mesh between the pinion and driving gear.
I guess it's not so simple if you want to make slotted holes that have ball bearings sitting in them for regular driven shafts/gears.
This comes from the clock making industry. A simple tool is made from a small plate with a slot. The unmounted gears fit over arbors and are moved in the slot until they mesh properly. At the bottom of each gear arbor is a sharp point that allows you to scribe an arc that represents the best gear center distance.