Okay, the first thing you need to do is totally remove the soaked foam. All of it has to come out.
Then you can measure for new flooring to be cut to go in. And if this were my boat, I would install some larger PVC pipe in the center of the boat from bow to transom to allow water to move to the bilge area to be pumped out via a bilge pump. And then I would buy some 2 pound per cubic foot type of mix and pour flotation foam and fill up everything to the new floor. That would make it like it was originally and ready for the water.
But before pouring in the new foam, make sure you have all the electrical wiring run, if any of it will be below the new floor. Never a better time to do that then before everything is sealed back up. And install any wires in some PVC pipe as well so you can pull new wires, or remove older wires, if need be now and in the future. JMHO