the bigger the vechicle the larger the tolerance for run-out,a huge truck will not be affected by .006" run-out ,but on a civic or something of similar size a .005" should be machined. and Bob, i'm prettey sure you made a mistake ...its more like .006" and you can still machine it if its in spec.
and you want to measure them in the deepest groves doesnt matter exactly where ,as long as the measurements are spread out.
and please for the love of god, dont go to any so called "brake Speacialist " places .they will just fuck you for your money.