I'd go back to where Nitrowarrior was taking you. It sounds like it might be a case of "garbage in, garbage out". If you have a fluctuation in the hot lead voltage then you WILL have a miss on the secondary side.

Voltage fluctuations on electronic motors are worse than on an old fashioned points based system. In both systems when the voltage drops you lose spark immediately (or nearly so). When power resumes it take a bit of time for the electronics version to get it's stuff together again, this stretches the event out and makes it more noticable.

Was the engine miss coincident with the measured voltage dropping down to 1V (or less)?

Where was the ground reference probe (black lead) of the meter placed when you were making these measurements? On the block or at the battery post?

With the probes placed in the location where you saw the voltage fluctuations try wiggling the wires/harness to try and simulate the vibrations experienced when the engine is running?

Cheers, Mark