My wife and I purchased an old farm house with the intent of remodeling it. We were planning to refinish the old wood floors. The floor is currently 1 inch native pine in fair condition, no sub floor under the pine. But we have discovered, not surprisingly, they were painted with leaded paint many years ago. We've painted them with heavy floor latex to lock the lead down (the recommended procedure as per our local health department) and to keep our 1 year old from becoming contaminated. I've also began screwing all the boards to the joists with 2 1/2 deck screws to firm things up. I don't think anyone has touched the floors since they were installed as nearly every board is loose and many of the square nails are popping out.

Anyway here’s my question. I’ve been reading that the maximum variance for floor flatness is 3/16 inch over 6 feet for new floors. As I mentioned above this is a 106 year old home and I know the floor boards have close that to much variance and in some places it will exceed that limit. What is the best way to correct for variation in the boards, considering sanding, or any thing that disturbs the leaded paint on the floor now is absolutely out of the question? I’ve considered 1/2 inch plywood sheeting, and/or a self leveling compound.

Plywood and asphalt paper / roof shingles would be the least labor intensive and will level it out quite well. Use the shingles and paper to raise and low spots, then screw the plywood to the pine.

Oops I guess I should have mentioned we are planning to install 3/4 inch solid wood flooring, either Red Oak, White Oak or Maple.

Another question While I'm at it. Can we install the new floor at a 45 degree angle to the old pines planks or do we need to keep the new floor perpendicualr to the old?

45º is a perfect for what you have to work with.