Good questions but the answers depend -

Is the boat going to be sailed at sea in potentially rough conditions?

oh yes i figure the coast of Alaska, out in the chain as far as attu
the remote islands in the arctic, the south pacific, down the west
coast of south America, the African continent, selected parts of Asia,
and the a few trips to the med.

If so, how many days of sea stores? Fuel and water requirements?

I am figuring 60 days of water (about 700 gal with a reserve, i have
not decided yet weather to cut this down due to water maker ) and
stores the longest transit would be the coconut milk run of almost
3000 miles.
fuel for 100 hours at working loads so call it 200 gal (hydro for
cargo gear, generator (augmented with solar and wind), water maker
and cook stove)

Are we talking about a 50 footer with full keel?
yes

What about the center hold - fish, dry cargo ?
both. depending on need.

Walk through or not?
not walk through.

How many crew?
max crew of four adults, mostly will run with two crew I expect kids
will be involved in here someplace.

Deck layout - pilot house, center cockpit, aft cockpit?

aft Pilot house slaved aux station forward of house at deck level,
center water tight hold, small coffin forepeak.