Sounds like you are about to do what I had to do. I was removing Wasp Nests, and I removed the carpeting and found that the flooring was a bit soft in places, so decided to get rid of the "loose" stuff, as I was exporting the lot home, from NY to Tasmania, and didn't want any surprises with Quarantine and Customs. Boy, was I surprised when I was confronted with the sight of thousands of live Carpenter Ants. Had to remove those, or hell would have broken loose if they were found. As it was, four eggs that I didn't find hatched on the trip over, and then the whole thing had to be fumigated with Methyl Bromide, at my cost.
At least the old timber and ply framing came out easily, as it wasn't that well stuck to the fibreglass, and it didn't look like it was Marine Ply that was used in the first place.
Now, I have a "New" boat.
Bruce.