How can I get rid of the odor if it has penetrated the carpet and a carpet cleaner isn't helping?

I am in the process of addressing this situation at home with urine which had soaked into the carpet padding and subfloor. I cleaned the area with Zep Carpet Shampoo for an extractor, literally pouring the solution on the flooring and then walking over it to get the solution to soak the carpet, padding and subfloor. Afterward, I used an extractor to get most of the cleaner up. I repeated with gallons of hot water soaks. When the rinses were relatively clean (the rinse never became clear), I applied a 50/50 solution of white vinegar and water solution and walked over the area again. Afterward, I used hot water soaks and the extractor to get the majority of the water out. Long and not fun!