On my web pages in my Source-code View, my categories show up before my Body Text. Is this a problem for SOE? And if it is can I fix it by cutting and pasting the categories beneath the text?

Well, no, It is good for seo. It will help you out for all your keywords, as your categories, like Hormone Therapy would be one keyword.

I would really prefer for my Body Text to be more prominant since most of the Words in my Categories have too much competition. This being the case do you still think it doesnt hurt?

Just try and fit a couple of your keywords before your navigation and you should be fine. Most sites navigation comes before there body text, so you are not alone