Find yourself a good scented disinfectant. Chances are if the stink is not going away or is only being masked by other smells, you have some kind of bacteria, fungus, mildew, etc. in there. A disinfectant will kill that stuff and mask the remaining scent.
The key to boots not smelling is keeping them dry so that stank doesn't have a chance to develop. Invest in a boot dryer, or build one, they are worth it will help your boots to stay smelling decent and be dry for your feet the next day. Or if you're looking for something on a budget that is a bit more portable, these puppies work pretty well.
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