I ended up doing a complete enclosure change. Used a 10 parts water to 1 part bleach solution to wash out the enclosure. Then I thoroughly rinsed out the enclosure (I have a very interested 11 month old kitten who gets into EVERYTHING). I went to Lowes and they recommended to use sticky fly tape traps. Told me to wait until my plants were almost completely dry and to water them with the same bleach solution to kill the eggs. By the time the spider plant I plan on putting in the enclosure is big enough, the bleach would have been broken down and completely harmless. So far, the tape traps have trapped over a dozen gnats!
When I went to go clean the enclosure, I boiled some water and took some of the old substrate out and put it in a large rubber made tote. Poured the boiling water over it and let it cool. Then I put Boris and Soyna in that (which they did not seem to like).
When I put the new substrate in, I used much less water. It is a bit dry right now. However, I want it to be unattractive to the gnats. I'll bathe my tortoises a few extra times this week. Once the gnat situation is under control, I'll add some more water. Of course, they still have a container of water to bathe in.
I really do not want to use any pesticide. I don't want it in the apartment. I honestly did not want to use bleach (again, I have a very cute but naughty kitten).