Transitionial doctypes are only meant for ten+ year old browsers. No new sites should be using a transitional doctype, so definitely go with strict.
Am till debating xhtml vs html, taking into account mobile users.
It doesn't matter much, especially if you are serving the xhtml as html. HTML5 will pretty much kill this issue anyway, as far as I can see.
While am asking, would you use a container div or header/main/footer divs by themselves?
Are you asking about HTML5 elements? If so, I wouldn't use them yet, as they only work with hacks at the moment—especially in older browsers like IE8 and below.
Otherwise, not sure what you are asking there.
EDIT: O, maybe I do see. Well, it depends on your layout. I would probably use those separate divs anyway, but if you want bands of color across the screen, then go with the separate option.