Re: Progress so far...
I do not believe there is any regulation that requires you to put back the foam in that size boat. But it nice to have. There are other locations to add foam, like under the gunwale, under the splashwell, and depending on your seat choices, you could fill in under lounge seats.
You are right that foam does mess up drainage holes. Given the options, I would leave the under floor area un-foamed and look at alternative above floor areas to foam. Plus, above floor foam helps keep the boat from flipping over if it does get swamped. In fact, this is what the coast guard recommends.
So, if you can see how you could add foam above the floor (which you can add at a later date), then leave the under floor empty and add the drainage. Plus, you can add hatches in the floor to store gear like anchor, fenders, etc .
Just something to think about.