Restoring 1939 oak flooring issues

We own a very nice "custom built" Georgian Brick two story home overlooking the eleventh fairway of the Washtenaw Country Club (founded in 1900). I believe the floors are first grade oak. They are made of very consistent short boards (2 1/2 to 3' in length) with no knots. If you look at the floor in the dining room which never had wall to wall carpet, it is a dark brown color and appears to have no shellac or varnish applied to it.

We recently broke down and moved all the furniture out of the master bedroom suite (2 walk-in closets and a master bed room in a 14' by 24' section of the house) The floor under the carpet was not dark in most places and had quite a thick layer of shellac which I'm in the process of washing off with denatured alcohol. The floor under the carpet at the entrance to the master bath (a wear spot which was dampened through the carpet by walking on it barefoot coming out of the shower for 17 years is very similar in color to the downstairs brown, but the rest of the wood under the shellac is looking like it is probably red oak, not white oak as I had guessed from what I see downstairs where it is exposed.

We had no plans to refinish the floor in our dining room, as it is in good shape and suits the oriental rugs carpeting the room and the lower hall. If I do nothing but lightly sand the upstairs floor after we get the shellac off, it is going to be a lot lighter in color than the one downstairs. My wife is not going to stop coming out of the shower with wet bare feet, and I'm convinced that I need to get a water resistant finish. We both agree that we don't like a shiny floor, so the surface finish will probably be one of the clear water based polyurithane finishes.

Now the questions...

1). Can I use an oil based stain to match the downstairs floor and then apply water based poly over it? If not, how can I get the floors to match?

2). Should I try to "fill" the nail and staple holes before any sanding and staining or just let the inevetable sanding residue fill the holes and fill anything that really sticks out after the floor is rough sanded with a "stainable" filler?