I'd been thinking about what what to do about the rot in the floor, I the problem was mainly with the top layer of 9mm ply, but some of the lower ply also had rot in the end grain.

After much uming and ahing I decided just to chop it out, its what I did with the boat so decided it would be the best option.  I've chopped it all back to good timber and where possible to a chassis support, I then plan to cut the foam back at least 6 inches to create and overlap for the bonding.