Only three sparks per rotor revolution on leading plugs?
 

I should be getting six, right?

What could possibly cause this? I already borrowed a good coil and ignition sub-harness.

Would I be able to learn anything with a commander?

3 engine rpm = 1 rotor rpm.
Each rotor has 3 chambers.
Rotor housings have 2 plugs, leading and trailing.
The two leadings fire together as a wasted spark configuration. Thus 1 leading coil.
Each trailing plug has its own coil.

Recheck your your faulty calculation!

The leading coil most definitely fires twice as often as each trailing.

Look at just one rotor at a time. The leading coil should fire the same amount of times as the trailing. If that's not occurring then something is definitely wrong. 3 sparks per rotor revolution or 1 spark per motor revolution out of each leading and trailing.

The leading system is a waste spark system. It fires six times per rotor revolution. The trailing fire three each.

This