Fortunately, on removing the first panel it became clear that the smell is actually in the old plywood deck boards themselves, not in the fiberglass hull.
On Monday I pulled up the rest of the floor. It was tabbed in along the sides very securely with about two layers of glass, which meant I had to grind it out with my small Makita grinder. For the first time in my life I used a respirator, goggles and ear muff style earplugs, and I was glad for all the protection. That was one very messy, noisy job. There is fiberglass dust everywhere.
The result, after removing the sole (that's the official term for the cockpit floor) was a clean bilge with no debris, water or damage of any kind. The stringers were laid up beautifully, with no messy glass fiber edges anywhere. Those early Skagit crews were obviously taking pride in their work.
I had only a couple hours this afternoon and spent them doing the last of the grinding and the start of the sanding process. I'm using 50 grit paper on the random orbital to remove all the loose paint and rough every surface for painting. Tomorrow, Saturday, I hope to have enough time to finish the sanding, clean everything thoroughly (there is dust everywhere), and do the cutting and fitting of the floor boards. Prior to screwing and tabbing them into place I have to get two lengths of 1/2" PVC pipe to run from the cabin all the way back under the floor to what will be a well for a bilge pump. If it sounds a little complicated, it is becoming so. Some discussion on the club web site today made it clear that I have to foam the voids between the stringers after the floor is down. Fortunately, that process can wait until after our San Juans trip next week, but the pipes must be in place before I start sealing things up.