Misfires will cause a flashing CEL that goes away when the misfires go away. I had a flashing CEL at the track when my oil was slightly overfilled and I blew a giant smokebomb at the track. When the smokebomb cleared the flashing CEL went away. It was very scary and the power dropped out for a second, almost like when the TC comes on. I think you are on the right track.
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