Getting good alignment of the FSB is much more difficult than doing the pins. The guys that do it professionally usually have some sort of fixture to accurately align it. I've done one myself without anything special, it took a lot of time. I put cardboard on the jaws of a pair of Vise Grips and used them to clamp the sight base to the barrel. I centered the carry handle sight then shot the rifle in by rotating the FSB.
I didn't do anything special on where to position the taper pins. You are right they can be too deep in the barrel or not deep enough, and I know the print calls for +- .005 spec, but in my opinion there is more acceptable leeway for proper function. I eyeballed mine for the center line of the drill to run through the intersection of the barrel and sight base. Then reamed them a little at a time for the pins to seat properly. I am very satisfied with the pin placement. Is it perfect? No, not by any means, but I'm doubtful most would ever know my fists of ham did it without anything special. Alignment ended up 1 or 2 clicks off from true zero on the carry handle. Access to something like a Bridgeport and some tooling could get you within the measurements called out on the print, and I'm sure is how John Thomas and ADCO do it. The pin placement on factory built rifles is ALL over the place for what it's worth.