Hi William;
Welcome to the wonderful world of Rocket Stoves!
I'll take a crack at answering your questions.
1) With the Walker cook stoves those are good clearances.
You may find on some days that you want a window open at the same time as you are heating the mass.
2)Personally I couldn't imagine not having a propane stove. But at our home hot plates and toaster ovens are out unless you want to use the generator.
Matt has talked about his ovens during stove chat live. I believe in his smaller stove, it is a "black " oven only and he uses covered cookware when he wants to bake smoke free.
You would want to check but I think his large stove might have black and white ovens.
The best way to learn about Matt's stoves is to ask him. You won't meet a more friendly helpful guy! He loves to talk stoves, especially his!
Drop him an email with specific questions. here is his website
http://walkerstoves.com/index.html
3)I think this one your going to need to live with. Vents at the floor and ceiling would "help" circulate air. Ceiling fan always helps.
Take a look at Matt's water heater plans. He has commented how it could be used as a masonry heater as well as a water heater at the same time... can't cook on it though.