My best suggestion is to ditch countersinks, if you're running 82 degree hardware, get 82 degree spot drills. A little trick for 82 degree tools is to shoot for 10% more in depth than you'd would with a 90 degree spot drill (which has a 1:2 ratio, theoretically). You'll usually get it within +/-0.010", then adjust accordingly. Out of luck if you're running 100 degree hardware though...
From my experience, single-flute countersinks are pretty useless in CNC. Like HuFlung said, they run eccentic...so they are hard to take into account what they will do. And 6-flutes countersinks are ground flat with a big minor diameter, so it's a crap shot what you'll get in size as well.
Chamfering tools, it's usually trial-and-error with adjusting the minor diameter offset or the depth. I'm always on the big side with the minor diameter so that the tool doesn't gouge the part, so my adjustment's almost always with depth. Corner radius tools are the worst!