The original hinges were too small, due to factory mis-alignment. Vans sent a new -3 hinge, which was too big. I started by trimming the hinge by about 1/4".
The ailerons had to be mounted to align the flaps. I had previously made the required bushings and assembled the various washers, etc., required. I set up the ailerons, then aligned the flaps to the ailerons. The longitudinal gap turned out to be about 0.270 vs the 0.250 called out in the plans. Pretty darn close, but the extra gap made a great trailing edge alignment.
Once everything was set up, drilling the hinges was pretty straightforward.
After drillng, the hinges came off for the required deburring and priming.