And here's a partial answer to my question

I keep saying why does the thrush/yeast rash keep coming back and why does he get an ear infection at the same time? I said to Kevin yesterday maybe it's all related. He just nods and "hmm"s. If there's such an over growth of yeast that allows the thrush and rash to come back maybe it's affecting and allowing or causing the ear infections? Possible? Yes.

http://www.nutritioninstitute.com/ear_infections.html

"Ear infections are caused by bacteria at the back of the mouth and at the
beginning of the tubes leading to the ears. There are both benign bacteria and
bacteria capable of causing disease. There are other microorganisms present in
those places, however. The yeast Candida albicans also lives in the back of the
mouth and at the beginning of the tubes leading to the ears. In summary, even though the yeast which aid the disease causing bacteria are at the back of the mouth and throat, all the yeast which is in the rest of the intestinal tract makes it easier for yeast to grow in other parts of the body. So eliminating yeast from the intestinal tract is necessary to reduce the yeast in the throat and mouth, which in turn stops the ear infections. "

Ah ha. Makes sense if the thrush in his mouth is flaring up and traveling up to the ear canals where it can breed in that nice, warm, moist area. Anyway...I like when I am semi-right or intuitive about things =)