If your shoes keep on stinking no matter what you try, this build for a UV light sanitising box could do the trick. You just need a cardboard box and some germicidal lamps.
When it comes to the bacteria that make your shoes stink, dryness and sunlight can help drive them away. This build from Instructables user 3dfernando uses the same idea. Once you've got the germicidal lamps on something to support them, you can stick them in your shoes and crank up the heat.
The foil around the box will retain the heat and take care of most of the little nasties crawling around in your shoes. For the complete guide, check out the link below.
UV Shoe Sanitizer Box [Instructables]