1. Do not countersink the holes. Use a countersink tool to de-burr just the edges of the holes. A file is not the right tool for this as it can remove material that is proud of the surface, but will not remove the burr that is inside the hole. Do not attempt to drift the alignment pins in further with a hammer and a punch. A hammer should be your last tool, not your first. Look at the photographs: the holes are round, they just have a burr at the surface.
2. If you powder coat a bore riding bullet and it will not chamber, this is a diameter problem, not a length problem. Determining the maximum COAL is great, but your not going to be able to do that if the cartridge can't even chamber. Ideally the section of a bore rider between the driving bands and the ojive is right around .300" (for a 30 caliber bullet) The lands of the barrel are at .300" inside diameter. If you powder coat the bullet and it increases that long nose section to .302" diameter you're not going to be able to push that into a .300" diameter tube. If you try solving that problem by seating the bullet deeper into the case you might end up with just a tiny section of the forward driving band ahead of the case shoulder, with an air gap all the way around the nose of the bullet and the neck of the case. There are lots of other reasons why trying to fix a fat nose on a bore riding bullet by seating it deeper is a bad idea: too easy to push the bullet completely inside the case while chambering (which will generate a bore obstruction), Massive gas blow by and gas cutting when fired because the nose section does not seal the chamber lead, the bullet will enter the barrel crooked because the nose is not holding it in alignment when it is fired, etc.
When you have a fat nose bullet, adjusting the bullet depth so that it will fit the chamber works good on spitzer, Loverin, and flat nose designs. It does not always work good on bore riding designs because you would have to seat the bullet very deeply. The reason that I suggested that Wolfdog make up a dummy round at the normal seating depth is to see if his powder coated bullets will chamber. If they do chamber he can adjust the COAL for best performance, and all is good. If the cartridge will not chamber at all, adjusting the seating depth is not the answer: having the bullet nose at the proper diameter is.