Nice job on the redo. I am sorry for the problems your are going through with the BIL, but as several people have already stated on here, Karma will happen.
A suggestion before you stain and seal the floors, I used a solution of 1/4 cup PineSol Cleaner and 1/4 cup Clorox Bleach in 4 gallons of hot water to mop the floors with, and then let it sit for 1/2 hour, then rinse and used a solution of 1 cup of Baking Soda to 4 gallons of hot water let set for 1/2 hour and then rinse the floor well. This should eliminate any possible odors as well as allow the wood to really accept the stain. To save yourself from having to worry about scratches I would use a good heavy duty verathane sealer once the stain is dry. It will be much easier to keep the floor clean as well, you will just have to damp mop it.
I looked at the before and after pics, I don't envy you the clean up, have had to do that on a few occassions myself to several properties before I moved into them.
A suggestion before you stain and seal the floors, I used a solution of 1/4 cup PineSol Cleaner and 1/4 cup Clorox Bleach in 4 gallons of hot water to mop the floors with, and then let it sit for 1/2 hour, then rinse and used a solution of 1 cup of Baking Soda to 4 gallons of hot water let set for 1/2 hour and then rinse the floor well. This should eliminate any possible odors as well as allow the wood to really accept the stain. To save yourself from having to worry about scratches I would use a good heavy duty verathane sealer once the stain is dry. It will be much easier to keep the floor clean as well, you will just have to damp mop it.
I looked at the before and after pics, I don't envy you the clean up, have had to do that on a few occassions myself to several properties before I moved into them.