go for the .040" as the others are too thin. get the total thickness of the wood & plastic decks together & scribe/mark the bottom of that thickness on the inside of the hull. if it was me, i would glue pieces of .040" plastic to act as shelf brackets for the new deck to sit on. also i would use the kit's sprues as cross pieces to prevent the hull from moving out & to prevent the decking from sagging. learned from doing 12 of 17 models using that Arizona for my OBB thread on the other site.
also bevel the edges of both decking materials from the hull casements & forward as that area of the hull slopes inwards which hopefully closeup any gaps you currently have with the white plastic deck. i do my decks differently to what you did with the white plastic deck as i scribed mine 1st, cut to shape then bevel the edges by the bow & stern so no gaps appear between the decks & hull. also i don't do actual wood decks at that scale but might do it on my 1/144 scale warships that have wood decks in real life.
as you are doing the pre-attacked & the memorial versions, why not do the attacked version before all masts, stack & deck clutter was removed? if you want to go a bit wild at it but not like me with my OBB/s, why not do all the various versions since she was built?
Well I don't have update on this build other than I plan to finish this next year, and I did finish, not one, but two models for the first time since 1982, more than forty years ago!!!
one is a Lindberg 1967 Olds 442, and other is an Italeri MB 339 A