Took all the clecos out of the rudder and deburred all of the match drilled holes. Used a single flute 100 degree hex shank deburring tool (DB04) in a Ryobi cordless screw driver as well as a hand deburring tool (BAT-196HDT). 

Also used a Cleaveland Tool drill jig (DJ25) to countersink the R-1006 trailing edge. When I countersunk the second side the match drilled #40 holes got a little larger but I understand this to be normal. There is no way to properly countersink the TE without this happening.

100 degree hex shank deburr tool –
http://www.cleavelandtool.com/Hex-Shank-Hole-Deburring-Tool/productinfo/DB04/#.Wm1GeainGHs
DJ25 –
http://www.cleavelandtool.com/Drill-Jig-for-RV-Trailing-Edge-Wedge/productinfo/DJ25/#.Wm1GsainGHs

EDIT : The safety wire holding the cage from spinning on the countersink is NOT a good idea.  It causes the countersink to heat up and the grease inside to get more viscous.  The holes will go deeper as the grease gets hotter.