That smell may not come out. The boards may have to be replaced.

Removing the odour has been done successfully on very rare occasions. You will need tremedous amounts of enzymes specifically designed for cat urine; a few weeks of daily scrubbing of said enzymes+rinsing to get this up. Remember, if the urine ran between the planks and penetrated the edges/undneath of the planks...or worse yet the subfloor, you will never get it all. Not unless you pull every plank, scrub down all 6 sides, scrubbed/replaced the subfloor and even possibly the trusses will you have a chance of getting it all. At that point, you might as well lay a new subfloor and new floor.

Wood is porous and can urine is highly agressive (ammonia is the least of the worries) which means it attacks and enters porous surfaces. Once in, it doesn't come out unless you cut it out.

Soaking the floors in a peroxide solution (25% peroxide to water), mopping it on heavy and sealing it off with plastic (allowing it to sit for at least an hour) then sprinkle a mixture of baking soda and kitty litter to suck up the moisture and odorous liquid. Let sit for several hours then clean and dispose all of the kitty litter. Then mop again with clean water- using a clean water bucket and a rinse bucket for each pass.

I would still encourage you to sand (or at least lightly screen) the floors after this application. Sorry, I know you just sanded but this will ensure removal of the surface layer of stains/uric acid that were brought up from the treatment that could soak through your paint coats.

Make sure to let the floors air out for a day in between your final preparation of the floors (either stain or paint).

Are you planning to paint the floors because you would like to do a bold color? Paint on the floors can be slightly more difficult to maintain than stain but can be a fantastic look. I would encourage you to stay away from browns. go bold, make a statement and have fun with it! There are also many colorful stains to choose from that might help you maintain the character of the floors but you will still have a fun new accent. The new colorful stains are waterbased (so they are much easier to clean your brushes and stain pads) but will also help protect and seal your wood and if you get a scratch they can more easily be touched up.

Scroll down to Waterbased to see some of the great colors. You should be able to pick these up at your local Sherwin Williams:
http://www.minwax.com/wood-products/stains-color-guide/

I would love to spec out Island spice, Antique jade or Deep Ocean for a client. Make sure to test the color (paint or stain) in a closet or unseen area before applying to the whole area.

Happy Floor Refinishing!