I started with the holes in the longerons as these are easy to access. I used the following process for both sides: I started with #40, then #30, then #21 and finished with #12. I would have preferred to use a reamer, but the one I have is too short to reach from above.
With the front spar bolted down, I moved to the rear spar and used a long #30 drill bit on the two lower holes. The drill block is v-shaped and cleared the rivets fine.