I replace the same floor section in my 68 Trade Wind. After final fitting, I painted top and bottom edges ( in to about 6 inches) with 2 coats West System epoxy resin. On the remainder of the surface I put 3 coats of a premium marine urethane spar varnish. I hope I don't have future leaks, but if I do the floor is somewhat protected.
FYI, I had to put the floor in in two pieces. the single piece won't slide into the C-channel. I split it over the street side frame rail. Used elevator bolts and self tapping floor screws to secure the pieces.
Finally, if you haven't done the work yet, I strongly suggest getting a piece of luan plywood and making your pattern from that. Get it fitting perfectly then cut the heavy floor from the luan pattern. A cardboard pattern is not stiff enough. Getting the heavy floor into the c-channel was a big job and having it fit very close helped a lot. Also I ran my router with a slight round over on the edges that go into the channel and it made the final install much easier.