Did you clamp the caps when you drilled them? If so how did you do it so that you didn't scratch the cap?
I have a drill press and clamp.
http://www.harborfreight.com/4-inch-jaw-capacity-drill-press-vise-30999.html
Safety glasses.
Punch pilot hole guide dimple.
I tape cap to avoid scratches.
I use 1/4" plywood scrap against jaw faces to avoid scratches.