That water can damage your diesel fuel injection pumps if it gets through the separator, and that's an expensive repair, x's2.

Your idea sounds pretty good to pump any water and sludge from the bottom of the tank. But I wouldn't do it into the bilge Dave, I don't see how you can keep diesel from going into the bilge and then out into the harbor. I'd see if you can get the bullk of the water into jerry cans for disposal. It sounds like what you were doing worked well.

Maybe what's left below the pick up won't be an enormous amount to lug? At any rate, you'll get the bulk of the sediments that are clogging the filters that way.

I can't imagine recent condensation adding that much water to the tanks. It's a great thing you haven't filled the tanks completely yet. Your system looks great on the blog and may have saved your engines already.