If the plug is not firing but fuel is being injected it will be wet for several minutes at least. When the problem occurs, pull over (safely) and pull the rear plug out.

With a carb the good cylinder could be wet. Not likely with EFI.

The two primary windings are measured between A and C and between A and D. HT means High Tension. Measure from A to each of the HT terminals for the secondaries. If the primaries are good it wouldn't much matter if you used A, C or D. You could also measure the two primary windings simultaneously by measuring between C and D. Expect twice the reading, or 1.0 to 1.4 Ohms.