After some consultation with more experienced builders, I found what part of the problem with my cheap nicopress tool is. If you look at this picture, you’ll probably see it too:
The outermost contact point on the inside of the jaws is too big. That’s making an air gap between the contact points at the other positions in the die. I used a file to remove enough metal from that spot to allow the dies to finish closing, and the end result was much better. All of test subjects now pass the no-go gauge, so I made the front cable for the left aileron. I replaced a few of the hinge bolts with rivets on the right side, and started going through the right wing to check for proper hardware and torque. In the whole process I only found one bolt that was the wrong size, but it was easy to fix. I started on the right front aileron cable before I had to quit for the day.