Don't hold me to it...
It's been a while since I did this, and I assume you are referring to when you drill through the gear leg and the gear mount. As I recall, I aligned the holes visually, then with an undersized rod, then slowly drilled with the prescribed sized bit (1/4"?). I used an extra long bit (12"?), which helped with alignment. Since the holes are already predrilled, the distance you are drilling is a good ways, and you are only removing a small amount of material with the final bit size, the holes lined up pretty naturally. I did put some light lithium grease on the mating surfaces to help me insert the gear leg, and that probably helped things move a bit to line up. Hope it helps.
I remember worrying about it too but, as with most stuff, no big deal.