Smell in 80 Series Landcruiser / LX450 - How to reduce, or get it out
We encounter this smell problem on many rigs. It is 90% of the time the stink is in the carpet.
You need to pull the seats, center consoles, and trim. Completely remove the carpet from the car to clean. Simple "Extracting" with a machine just isn't as good.
Best is to separate the factory sound deadening from the carpet and toss it. You can install better aftermarket foam style deadener later that doesn't impregnate by liquids. You can do a search for these materials such as second skin, etc. Some have heat blocking as well.
Pull the carpet out and lay it on a clean concrete surface. You need to clean the carpet well with scrub brushes and carpet shampoo. Afterwards hang the carpet over a sawhorse or other tall device to rinse. If you have something with some pressure to hit it with water, it helps out a lot. You would be amazed how much filth drops out of a carpet that "looks clean". You can just imagine what will come out of a stinky one. Next clean the entire metal floor area. You don't want to drop your clean carpet on a stinky dirty floor.
You should see a serious improvement on odor for sure, and humidity will go down without the factory deadener. That moisture retention has also been known to rust out floor boards as well- so don't be surprised if you find some surface rust. If so, seal it with some POR-15 or similar before reinstalling your carpet.
We do this to almost every cruiser we have, even if it doesn't "need" it. It really improves the long term love-ability of your cruiser.
*** Of course fix where the water is leaking into the cruiser first

This could be from a multitude of reasons not limited to: The windshield gasket, drain plugs in the floor allowing splash up, sun roof leaking, condensation dripping in from climate control system, or more... ***
Wish You Luck On Your Endeavor!