Otherwise, the rot fungi in the bad wood will just move over to the new wood and you have rot again. Yes, I would put drainage holes in the bilge bulkheads. At least that will let the water come aft where you can get at it. I don't like carpet on the decks. It traps water, and there goes the rot again.
Wolmanized lumber is fine.
If you're using ply, be sure and treat the edges especially with the CPES to water proof it. It's as easy to use as anything and has a known structural strength when resin-coated. Right now you're deep in the middle, and it's hard to be really specific.