Hi Andrew
I removed the deck of my timber mossie with a router. I put a hole saw through the deck first then set the router at the exact thickness of the ply I found there.
Using a TCT bit I then ran the router over all of the deck that was attached to something. The TCT bit was essential as it ate through everything in the way including the nails.
This left only a very thin bit of glue over everything including the foam bulkheads. Any imperfections were then sanded ready for redecking when all the faults were fixed.
Roughly cut out the correct shape from a new piece of ply and glue and nail on ( make sure to use Monel or copper nails!) when dry use the router again, different bit this time with the little bearing at the bottom, and run it around the edge of the gunn'l.
A bit of a sand and a paint and your done... Sounds easy, probably takes 3 hours plus paint and the hardest part is putting the first hole in your Mossie!
Trevor