Knowing the area where your pump out fitting is located, I know that there is little room from below to address the coring issue, but maybe if you enlarge the cut-out and remove a liitle more of the ceiling liner, you can work from below without having to disturb the beuatiful two-tone deck. There may not be as much rot as you think, or perhaps you could dig out enough, dry out for awhile, then use a penetrating epoxy like "Git-Rot" to soak the rest of the balsa. Working upsside down like that can be a pain, but using parchment paper, keeps you laminates from sagging/dripping while they cure.
Here's a link to Git-Rot:
http://www.jamestowndistributors.com/us ... atch_type=I have no affiliation to this product.....