Look up 'Coopers or Vauban corners'. The idea is that there are projections on each corner that allow coverage of the adjacent corners, and no dead spaces.

While I wouldn't buy it new, if you can find a copy of Joel Skoussens books on home design, they may have some useful ideas.

I'd plan on a full basement, with 'bump-outs' outside the home floorplan for a generator room, cold room/root cellar, and maybe an escape tunnel. Have a well or a very large cistern in the basement. Building fallout protection into the basement is trivial - during construction. It's also pretty damned cheap - during construction. Your wife will no doubt have plans for the kitchen, just make certain it's big and I'd put in a dedicated adjacent room as a pantry (not some little cupboard), and consider a deep sink, counter space and outlets in the pantry, too. My wife found the kitchen of her dreams here:http://thepioneerwoman.com/homeandgarden/category/lodge/

Be smart designing the house. For example, the vast majority of things that need to be laundered come from the bedrooms - so why have the washer/drier in the basement? Keep them near the bedrooms and skip carrying the clothes baskets around. For the septic tank, get the biggest you can. Mine is sized for a 20 unit motel.

If you're on propane, get a couple of tanks, and berm them in. If you have suitable wind, consider windpower: Western NY isn't exactly the best solar location I can think of. Instead of one big generator that can run everything, consider two smaller generators that can each run most things. Get the manuals and overhaul kits for them, build a very good cooling system and air filter, and if it doesn't have an hour meter install one and change the oil and filter religiously. If you can find one, get a Listeroid motor/generator head: they will run on nearly anything flammable.

Goats are easier to handle, grow faster, and the miniatures are basically single-meal sized while producing enough milk for use. Also, if one doe dries up, dies, gets sick it's not a tragedy - if you have others.

And good luck!