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I had the same thing happen to my electric water heater (as far as the red flashing light). I had to contact Whirlpool and they sent me a new electric board. They actually sent me two, and I can take a picture of it if you want (I have no idea what make/model your heater is).
The problem went away after that. But...you already said some electric parts were replaced so maybe that was already done?
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