If you haven't already done so I would scope the ecu earths along with the primary.
Years ago I had a fault on a test rig that was losing an earth to the amplifier intermittently, every so often instead of the amplifier switching and pulling down the primary to earth it gave a very similar scope trace as you have.

When the earths were tested with a DVM no fault was found but when tested with a scope it was clear to see every time the fault occurred the earth voltage went up, the current went down and the HT voltage reduced as the coil failed to energize correctly. Another earth bridged to the correct side of a bad connection cured the fault.


Graham