Ok, thanks guys. I’ll try and isolate a bad coil and report back.

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1 hour ago, Kent Ashton said:

I have had a coil go bad that takes out two cylinders...

Anytime that two cylinders stop working with the LSE ignition, it's almost certainly a failed coil, as Kent says, since the system uses a waste spark configuration that fires two cylinders at the same time from each coil. First, use your EMS to monitor the EGTs when you do the runup on the EI alone and verify that two cylinders (1 & 2 or 3 & 4) are failing to run. If it's only ONE cylinder, then it's not a coil - it's probably a plug or wire. If it IS two cylinders, then swap the coils, and determine if the failed two cylinders follows the coil.

If the failure follows the coil, replace the coil. If it doesn't but it is two cylinders failing, then the box is suspect (although there's a small possibility that two plugs and/or two wires have failed).

I have had a coil go bad that takes out two cylinders.   Also had corrosion in one of the coil towers that was fixed by a thorough cleaning.  The LSE Box can go bad if there is a broken chip connection in the box.  You would probably send the box to Lightspeed for a check if you suspected that.   I would pull the plugs, ground them on the engine and check for a spark as you pull the engine through TDC.   Carefull with that mag—sometimes they get ungrounded and also fire.   Crank Triggers are pretty reliable but the mag-hole trigger can have problems.