Finally figured it out. It's not bee poop, it's just pollen. I live in a rural area with a lot of trees, though I don't park under a tree. Throughout the day and night, pollen and other organic matter dust settles on the car. When morning comes a layer of dew forms on the cars surface. The organic matters starts to dissolve in the dew. When the hot summer sun hits the paint the dew starts to bead up into water droplets with the dissolved pollen. The sun cooks away the water leaving baked on concentrated pollen spots. If you wet them and let them soak you can scratch them off with your finger nail.
The only way to prevent them is by using a car cover or getting up around 7AM and using a product like EcoSmart RU to wipe off the pollen dust before it cooks on the paint. Or, wash the car every morning...
Once it cooks on the paint you really need to soak the spots to remove them with a cleaner of polish. I would suggest getting up around 7AM while the dew is still on the car. The spots will aready have been soaking for a few hours. Wash the car and then spot clean with EcoSmart RU (which seems to dissolve pollen pretty good). Remember to leave the EcoSmart RU soak on the spot before wiping off. The extremely stubborn spots will need to be removed with something like Meguires D300 correction compound on a microfiber towel.
So far I've tried several different waxes and surface treatments including F11 and Meguires ultimate. Nothing prevents it from happening and nothing makes it easier to remove.