Yesterday I did almost the exact floor repairs you are speaking of! My "subject" was a 1986 31' SOV with 5/8" flakeboard floor.
The previous owner pulled (and threw away) everything foward of the kitchen. The floor had moderate water damage mostly from an improperly installed vent. He became overwelmed by the project, and left it sit for a couple of years.
I cut out a 16" square of the worst area. I could stick my finger through it! This happen to fall directly above a cross frame and the main beam. Afer cleaning up the mess, I fould the only rust was the screws. These had to be ground down. I put in a couple of joiner plates and put the patche in. Total repair time was about 1 1/2 hours.
I also had some "crispy" surface damage further foward. This really wasn't that bad, and was out of the main traffic area. In fact, it will be under the gaucho. I simply scrapped it down, soaked it in fiberglass resin, added some cloth, and let it dry. This will be plenty strong.
I also plan on adding a layer of 1/4" ply just to give the floor a little more stability. The floor just gives more than I like. It's probably fine, but it will just feel more solid. Mine will have carpet. If I was doing Pergo, I would probably skip the plywood.