Ken,
I was reading a while back on the development of drilling or boring technology and how it related to draw boarding. The author described that the process was to drill through the first side of the mortice at an angle and then out the other side perpendicular to the sides being drilled through. I was puzzled as to how it was possible to drill one hole at two different angles but if the tool used had a short bit, something like I imagine a spoon bit could have, then it sounds more plausible. This may also have bearing on your question of alignment, but to add to that it would be helpful to begin with a sort of indentation hollowed out with a gouge or chisel. They won't register-ate me on the CF forum so I add my 2 bits here.

Greetings,

Don Wagstaff