Had a nice conversation with Eric at Vans and his recommendation was to make a doubler to place on the top of R-1003 B to bring it level with R-1003 A, a second doubler for the top of the first doubler and also cover the rivet hole in R-1003 A, along with a third doubler below the top flange on the rudder spar.  Once all of that is complete use a cherrymax rivet and call it good.  I ordered the cherrymax rivet gauge and made the doublers then fellow RV builder Josh came over and had a better method.  We took several longer rivets and “pre-squeezed” them to a larger diameter in the hand squeezer.  Found the one that filled the oversize hole the best and then shot them in with the 3x gun.  This provided a good result we were both happy with.  Of course I sanded out the smileys in the R-1003 A/B prior to doing this and later came back in and brushed on primer. 

Did not end up using these doublers.

View of top two rivets with smileys sanded out of R-1003 B

View from below of rudder spar flange (spar goes from left side of pic to center and R-1003 A/B from right side to center).