Those are the (CVTC) intake timing control valves. If the two wires that run to these were shorted together(one is +12v other goes to ECU) then when the engine is turning, the ECU's driver for them would get smoked as its trying to switch the battery to ground. As with the coil example the driver IC could get collateral damage. You said that the harness was repaired and the ECU was replaced after, if so then the next ECU should have been good to go...but if these two wires are still shorted together, each time the engine starts to turn you blow another ECU.
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