I think the problem you experience with spark plugs in, is that the two missing teeth are hard to detect on the revolution where it occurs close to TDC of one of the cylinders. Any chance to move the Ref-Sensor pickup angle to somewhere the crank speed will be fast? You should be triggering on falling edge with that pattern.
I don't see how you can run a 3 cylinder engine in wasted spark (2-stroke) mode since there will not be the same number of TDC events on each revolution of the crankshaft. I would think that you would need sequential injection / ignition and to do that, you will need a sync signal.
Can you find a way to fit a sensor to the camshaft? I suggest reading the help for Mode 7 (I think this is what you would use) -- there are restrictions on the Sync signal timing). It could be a Hall or Magnetic sensor that just picked up one lobe of the cam. Here is a picture of a hall sensor mounted to a valve cover that can detect a Cam lobe:
https://www.klrchris.com/klr650-fuel-in ... on-sensor/Good Luck!