I have had some experience with properties similar to this one. #3 - we tried a similar treatment on the carpeted ares but ended up having to replace the wood/subfloor after removing the carpet.
#2 - the problem with baseboards, trim, and sheetrock is they are porous. So even though you pressure washed them until they gleamed, it doesn't remove the urine that soaked into the wood. You may need to replace all of the baseboards. And we had to cut the sheetrock about twelve inches from the floor and replace it because the sheetrock had soaked up the urine. You can use Kilz on wood and sheetrock, but it will not solve the issue on heavily-soaked areas that have been exposed to the urine over several years. I know you have already put in a large sum of money on cleaning and renovations, but this is something to consider.
Also, consider having a service clean the ductwork and whatever HVAC system you might have. That smell can soak into these areas as well.
What about doors? Often the bottoms of interior doors have some buildup as well.
No jokes here. Cat urine is the worst, especially when it has been building up over the course of several years. Good luck to you sir.