Here's a few things to consider...
I can't help with after the fact and what to do with your current problem in total, but starting with DW and I, we tell everyone that BOTH genders must sit on the seat when using the toilet and to make sure there is some water in the bowl and to flush with plenty of water. Initially most people (especially the guys) are put off by this but this policy really works well. First time visitors need some instructions on how to prefill the bowl (if needed), then how to flush plenty of water and then prefill the bowl afterwards.
DW used a Clorox Toilet Wand and other general bathroom cleansers so I'm pretty sure your cleaning procedure is sufficient. With the toilet pretty much a vertical drop to the tank, if you flush with plenty of water and use a tank deodorant then the drain may not be the problem.
If you already do these and you still have odor it sounds like several possibilities including a seapage leak where fluids have found a way to leak out and into the flooring. This might entail taking the bowl off and looking for problems. Or if you do not use a tank deodorant the odors may be coming back up from the tank. Also, the black tank vent might be compromised some way and is not venting the odors upwards and outwards but this means a visit to the roof.
I hope other members can help you on how to do address other possibilities.
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