Tom, we've got the shower in a wood-interior boat, original. I looked at the situation in Alarm (a clean slate there), and I've paid some attention to more recent boats. I think you'd be ill-advised to modify so heavy-handedly as to try to build a separate shower; there's insufficient room, and none to spare. Fatter, more recent boats like a Pearson 36x have nice separate showers which are marginally big enough, all fiberglass inside and so on. Brewer-designed Morgan 38s are bigger than ours, too, and the separate shower is miserably small and a tripping hazard at the sill. Our Le Comte has a lovely all-wood head and a shower; there's a fiberglass pan under a lovely teak grate which, I think, is piped to the deep bilge (which I don't think you have). In any case, that's a lousy detail since hair and soap sludge will not help the bilge pump; better to have a sump and accessible separate pumped into a handy through hull. The Challenger and the North East 38 share the unhappy detail of the mast running through the head (cold, hard to seal to).
Negatives to cure on the N E 38 and to avoid with whatever you folks decide to build: figure a way to shunt all shower water down the sump rather than down bulkheads and the mast; that stray water will ruin the maststep, the wiring, and find its way up into the wood through the endgrain in the bilge. I had been ruminating on building an upper pan, 'flashed' (as roofers say) to bulkheads and to the mast (like a deck collar). Adding to the problem is ensuring good ventilation under such a watertight floor, and access. We have a shower curtain which, if you use it, directs most water past the counter and the throne, but it's pretty yucky to touch and tough to grab something through it. We wipe all the surfaces down and that seems to be sufficient for what shows. One way to cure the ills of the wood in water is to coat the wood everywhere in epoxy; I did a bathroom floor in antique heart pine and it's perfect after 5-6 years. Two layers plywood subfloor with the top surface covered in epoxy, the pine bedded in that epoxy, then all sanded out and coated. The wood is encapsulated. Tough for you to do now, Tom; easy for David on Alarm.