Urine will stain the flooring up to a quarter inch deep, so sanding it out completely is not practical. Sanding the surface can lessen the smell, but if you get close to the bare wood it still smells. A solvent based finish will help seal the smell, like universal sealer dewaxed shellac. Then you can finish with poly-urethane. I prefer to stain the floor a dark color like walnut so the dark urine stains don't show up so badly. You might consider covering the floor with 6 mil plastic to seal the smell and laying a laminate floor if you find one that looks nice. Laying a new floor over a sub-floor is a lot of work. You may want to get a book on finish carpentry so you can understand the details involved. Renting a stapler and using refinished flooring is the best value. Get the color that you like and you will never need to sand to bare wood to refinish. Prefinished flooring has finish that is better than what you can buy in many stores and holds up well. Add another coat of finish in 30 years, if you take care of it. Don't worry about how thick the surface is. If you are not going to lay flooring over the stairs I would stay with 3/8ths inch thick, so you will still keep you steps up to code. A power miter box saw, air compressor and finish nailer will do most of the work. An electric planer will help scribe fit to the walls. With engineered flooring you don't usually need to add extra trim against the walls. Take it one board at a time as you get started.
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