1. Agreed
2. For activated carbon, we just went to the local pet store. The package will have some fine silt which typically settles to the bottom I suppose, you can try to avoid. Outdoors, we scooped up carbon and put the bits into 2 wide bowls. Then moved the bowls into the car.
3. I would assume the recommended ozone pro had all the equipment.
4. Directly cleaning the evaporator with a specialised foam can work very well indeed. Thing is the coils get wet so are great places to collect dust, mold, odours. We used Toyota’s evaporator foamy spray by crawling under the car, spraying into the AC drain hose, and whatever else Toyota instructed us to do. I don’t know if that is the same procedure for the LC500 but the concept is the same. Some coil sprays require rinsing so avoid those IMHO (without rinsing, they may corrode the evaporator and I suppose they would leave a more dirty residue). There are some good YouTube videos showing how dirty AC coils get and tricks for cleaning car evaporators; it usually is pretty easy.
5. Toyota makes good filters IME. Wix is also a good brand; they have different lines (e.g. regular, heavy duty, carbon).

The ceiling has a lot of surface area and seems to be a popular collector of smoking odours in cars. I don’t know how one would clean that robustly. Some headlines seem to loose adhesion and the cloth droops over time, so hard scrubbing or steam might not be fantastic, I suppose. If you try to clean the headliner, I suppose you want to cover the seats and rug with a plastic tarp to prevent transferring odour. Removing some headliners seems “difficult” but I don’t know on your car. New ones are expensive so one option is to have local auto upholstery shop advise (e.g. cleaning or applying new material). Everything is so expensive these days. There are adhesive sprays if you want to replace the material but getting a perfect unwrinkled fit looks difficult for the DIYer.

--> I can’t imagine how frustrating this is. Especially as this is a premium car, the issue was hidden, and you have done so much work to remediate.

We test drove some cars that smelled of smoke and some with a perfume smell. The car we picked up had a musty smell that we didn’t notice for a few weeks and couldn’t locate. After all the cleaning research & execution, the car just smelled like must and several commercial cleaning scents lol. Eventually we found the culprit! Driver’s door had collected water inside (probably entered via broken outside mirror housing) and the drain holes were clogged. We removed the door panel, drained the water, scrubbed inside bottom of door, cleared the drains, replaced the mirror housing. Car still smells totally neutral and is extra clean too.