Yes, cats can smell spay/urine even after normal cleaning fluids are used. Your kitty is merely trying to assert that this is still his territory, by spaying the spots he smells.
Pick up "Natures miracle" at your pet store. It's a product based on the design for the cleaning fluid they use to clean up at morgues.It breaks down the basic enzymes, so even kitty can't smell it.
The shedding you'll have to live with and just brush her daily. Is she receiving a good quality cat food (i.e. not one of the grocery store brands that contains as the main ingredient ground corn?).
As far as the inappropriate urination, make sure you clean up the area so the smell of the urine doesn't remain (don't use ammonia). The cat will continue to be attracted to these places. One thing you should seriously consider is a veterianarian visit to rule out any physical reasons that your cat might be missing her litter box.