Isopropyl Alcohol poured onto carpet will remove alot of stains and odors. You do have to pour alot, then dab--don't rub or use pressure. You may have to reapply later, but alcohol evaporates and (hopefully) takes away all of the odor and stain. There is also a product out called Pets and Kids which can be added to your steam cleaner. This worked great when my neighboors sled team accidentally got into my home and had a spot marking contest.
First check for urine in molding, wood sink base or other absorbing material before you do anything drastic. Hopefully this will be your problem.
You may have urine under the tub, sink, toilet, or other hard to reach areas. You didn't say what kind of flooring is in the bathroom. If it is tile, wood, vinyl, and carpet, it may all have to come out and have a new subfloor put in or use a sealer such as Kiltz on the floor. Then put in a single piece of flooring (not tile, ect) and caulk around all the fixtures as they are replaced.
Good luck and Bless you for taking care of your mother.