The problem is in the pad and in the slab. When you do rip out the carpet you will probably need to have the slab sealed. I cleaned mine with bleach repeatedly first and it still wasn't enough in one room. I had to seal the slab. Keep the room blocked off at all times...at least the problem won't get any worse until you get it all taken care of.
My cat was not fixed for a long time and he did really well until we moved where there were previous pets...he sprayed on everything...even my clothes...and I had him fixed. He never sprayed again after that and he was about 3 at the time.
We tried everything on the carpet but nothting worked. On my couches I used a combo of lemon juice and vinegar and it worked wonders...we were sure we were going to have to get new ones but we are now all clear.
Good luck...maybe you can pull the carpet up with the promise of new carpet it he very near future and just leave the slab? At least you can bleach that for temprorary relief!