HI Missa,
Sorry to hear about this. This is very strange. Is it possible for you to switch themes for maybe a day or so and see if that helps narrow the problem. If these queries stop than at least you will know that it's the theme and you can dig a bit more.
Failing that, it sounds like you may need to hire someone who could look into this. Your theme might be running deprecated code or unnecessary queries. I'm only guessing though... I'm not 100% sure.