Have tried turning off the power for about an hour and the code will not clear.

I have also tested the flow pump, by connecting it's leads directly to the main power terminals, and it works OK. I have also tested the flow switch by disconnectiong it from the circuit board when testing the flow pump, my ohm meter shows it's contacts are closed when water is flowing.

What do I do now?

Most likely, replace the circuit board - based on what you've posted.