Hi Brett,
Vertically, positioning of your first one as high as the thickness of the crown inside will allow. The next two roughly 12mm-15mm apart. As long as you position the holes so the bridge always covers them. On the outside of the piston I always twirl a much larger drill bit in holes to ”Just” remove the Burr from the hole edges. Make sure you have removed the inside burr as well(I use a pencil burr, dremel sort of thing), so it doesn't come free latter and become "foreign body" for a "score"
Yes definite chamfer and radius all ports, especially to create lead in for piston ring on any ports it passes.
