Each hole in the 8 struts receives a counterbore for the head of a connector bolt/nut.  Some counterbores are on the outside face, which are where the struts fasten to the feet and to three spacer blocks along the length that will help provide rigidity to each upright.  The remaining holes receive counterbores on the inside face, which are used for fastening the climbing components.

I started by choosing which side would face outward on each of the struts and placing that side up, and then worked out the location for each of the spacer blocks, using some domino scraps to help visually with the best placement.  These columns of holes will get a counterbore.  (Not shown is the counterbores already made at the very ends where the last two holes on this side also get counterbores.)

To make sure that I got all the counterbores in the right holes, I used a piece of masking tape over the column of holes, and then cut the tape between pieces.  When using the drilling jig, the masking tape will show the target hole.

This process was repeated for each hole on the outside face.  To drill the remaining counterbores on the inside face side of each strut, I used a strip of tape to indicate the location of the counterbores on the opposite side.  This time when using the drilling jig I avoided the holes that were covered with masking tape.  Fortunately, I was able to place the locating plugs in the jig so that they always fit into the holes with the tape, which essentially eliminated the possibility of placing a counterbore wrong.

Even with 200 counterbores total, the process went quickly and smoothly with the jig.  Once my JessEm stock guides arrive, I'll get them installed on the router table and make the thumbnail edge profile on the struts, cut them to length, and they'll be done.  Except for sanding.  There's always sanding.