If I were taking-on such a project, I would probably follow Leo Fender's example: Start with a body blank with an area left where the pickups can be installed and moved-about. Also a bolt-on neck. Have you even seen pictures of his peg-board instruments? Leo could install pickups, replace them, move them towards the bridge or away without even loosening the strings! By experimenting this way, he could determine his preferred positions for pickups, pickup types, and pickup combinations.
You will still have a lot to figure-out as far as wood combinations etc, but at least if you know EXACTLY what you want to do with your pickups, I think things will go easier. Or of course, you could start with a really pretty Alembic, and just rout-away... but then if it doesn't come-out quite right, or maybe just leaves you wondering what if I... , you have de-valued a much more expensive instrument. AND your experiment still is incomplete.