Stop in for a cup of coffee

I know you changed the filters, did you clean or change the pre-screens? If you had water in the system, they likely gummed those up.

Also, I would take the lines loose at the cylinder and manually move the cylinders to flush out any other water and what not.
Did all that was definitely a milky mess. No idea how that much water got in there. Think the pump is shot, I just don't have the right tools to diagnose it. They are picking it up this afternoon.