Todd,

I am (woops, was) a custom home builder. We do ton's of wood floors. I suggest trying to contact a wood floor company and pricing a full refinish. These guys have all the equipment to do the job and deal with the mess.

Barring that, try talking to them with regard to what they use. Rent the equipment to sand the entire floor and do it yourself.

There are two things that I see floor finishes affected by...

1 surface prep -
Working in one area of the floor usually causes an uneven finish, or a new finish area that flakes up because it did not bond with the old finish.

2 TRAFFIC WHILE CURING-
Once you finish the area with polyurethane you MUST close the house and keep out until the whole of the floor is dry. Not tacky, but DRY. It will pick up dust from doors being opened and show forever. Finish the floor and get a room for a day or two. Motel 6 will leave the light on for ya'.
Plus that stuff stinks, and really isn't that great for the mind and body.

Good luck