First of all I am really sorry you have to go through this.
The poopy thing sounds like a power struggle if you ask me. He knows he needs to go, he knows where to go, but has decided that he wants to go in his diapers and is rebelling from your instruction. I would run by the library and pick up a few books on toddler rebellion (I like Dr. Dobson's approaches in most cases, but you are a different person than me and your child is different than my child so you might want to pick up multiple books by different Christian authors).
The chocolate milk thing is just plain unhealthy (though I let my daughter do the same thing with white milk so... yea). I would stop buying chocolate milk and only buy white for a while (who knows, maybe he wants the chocolate because it is sweeter than normal food). I would also start offering him water first then milk. 3 year olds should only get 16 to 24 oz. of milk a day. What I had to do is hide the gallon of milk in the back of the fridge and pour out 24 oz of milk into a water bottle (2 water bottles really because I only had 12 oz bottles, but who cares). I then gave he as much milk as she wanted until we "ran out" of the two water bottles. I let her inspect the fridge to "make sure" that we where out (the milk was hidden in a paper bag in the crisper and had carrots on top of it). Since we were out she knew that no amount of whining was going to get her what she wanted and she started eat real food again. In fact on the third day she started asking for water instead of milk and we only had to do this for about 5 days.
I hope that helps.
And of course I would pray. God Bless.
Edit: I found this on 3 year olds eating recommendations http://pediatrics.about.com/cs/agesstages/a/three_years.htm