I just bought a house with much the same issues. In fact the neighbor said that the people would let the dogs inside to relieve themselves. For me since it was a foreclosure the bank had already stripped the house of all carpet and padding. On day one I took a garden sprayer and mixed a heavy concentration of commercial bleach and water. I sprayed everything in the house. Be careful, the bleach mixed with the ammonia in the pee and caused a mild chlorine gas ( which may have helped the smell but didn't do much for my lungs). Today 3 weeks later it smells like new construction even after being closed up for a few days. As for fleas, one treatment will not typically kill fleas due to eggs that are continually being laid. I would suggest a reputable pest control company. Good luck!
