Pet urine stains are very difficult to remove from hardwood floors. In two houses we have had to strip the hardwood flooring, replace the wood and then refinish the stained areas. One house was so badly stained (awful smell!) we had to strip the entire floors of the living room, dining room, entry and two bedrooms. Part of the problem in replacing is that the new hardwood may appear different than the surrounding areas.
Re the carpet pad-you may find help on a carpet site or in a carpet store for advice on removing the stuck padding. Again, you may need to replace the hardwood here, as well.