the countersink isn't that big a deal.. sure it's a little lost volume, but not a killer. If it bothered me, I'd degrease thoroughtly and fill it with JB weld.

To the OP, just get a "long series" 3mm drill bit. For sure sounds like your seal needs replacing, but any port less than 3.0mm on a 12Fp springer, especially on a 27mm bore, just isn't going to flow efficiently, so you may as well do it when you have the piston out.