My experience and many discussions here at Sams suggest there are at least three possible sources of stinky interiors:
crud in the bilge (including refuse, open foam under tanks which gets soaked and smelly over time, and oil sludge/water mix);
potty stink (toilets, hoses, holding tanks);
water intrusion inside hulls and decks which leads to mold/mildew (outside leaks-windows,stanchion fastenings,hull to deck, etc- and sweating in cold weather climates).
For example, my 48 ft YF salon roof sweats on the underside and water drips from around the sides when I am aboard with interior heat on and outside weather is in the single digits. A neighbor live aboard with a '70's era 58 ft motoryacht had the same issue..he used to tie a thick thermal insulation blanket used for construction over his salon roof...that limited the temperature differential enough to stop his drips....
So finding the cause may not be so easy.