Yes, you have Alternator Driven Ignition, of the capacitive discharge type. There is a troubleshooting procedure on the CDIElectronics.com website. You likely have a bad switchbox, but check it out first.
Be sure and tesht the stator and trigger. I had a 90 horse inline 6 in the shop today with the exact same problem. No fire on 1 3 and 5. There should be two switch boxes. The one on the top controls the effected cylinders. Ohm test between the blue wire and the red wire should be around 6200 ohms on RX1000. Then test between the red wire and ground should be around 50-60 wiht ohmeter set at Rx1 do the same test on the wires to the lower switch box if they ohm out the same then the stator is ok. If the stator is ok then you can simply connect trigger wires from the bottom switch box to the top and see if you get fire on 2,4 and six. If you dont get any fire the the switch box is bad. Hope this helps
