I think the gears look best when the handle shafts are perpendicular to the curve of the back of the scroll. But this can put the handles a little too close for comfort, so you have to play around with them a bit. ideally the pegs when fitted will not cause the strings to rub against the next peg, but this is tricky to achieve as well.
To drill the holes perpendicular to the cheeks, I mount a piece of 4" x 1/2" timber in my drill press, then with the timber inside the pegbox, clamp the pegbox edge to this. the cheek is now perpendicular to the drill and the timber serves as a backing piece to stop the drill from splitting the inside of the cheek.
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