Separation Anxiety and Dog Agression with a Boxer Mix (long)

I'm sorry if this is a little long.  Maybe you guys can think of something that I haven't nor the 17 other trainers and 2 behaviorist I have spoken to have.

In July of 2007, I adopted a 2 1/2 yr old neutered male Boxer mix.  I adopted him from an animal shelter that everyone warned me about.  I guess they usually adopt out ill dogs, but Carter came to us with nothing except food allergies which was easy to fix.  I have no background information on him except that he was adopted out once before me but returned in a week because their dog didn't like Carter.  You can tell Carter was abused before we got him.  He is scared of anything whip-like, brooms (which we have finally overcome) and loud voices.  He isn't scared to snap at you if he does something "wrong" a you raise your voice at him.

I'm not sure if you can see websites from where you are reading this from but http://pets.webshots.com/album/172417748ihqGHy If you'd like to see him.

From day one he had Separation Anxiety, but it never seemed severe enough to worry about, I guess that was where my first mistake happened.  I also started to notice that when we would pass dogs on the street Carter would try to pull me over to "greet" the dog but start to growl when he got close.  I found out on Christmas day that he can me around other dogs and play as long as I use a muzzle to introduce him to the other dog.  I did an obedience class with Carter in mid-September which he did "ok" in.  He was always trying to go after the other dogs in class and any dog that came into the building, but a correction from me usually kept him out of trouble.

During said class, I was told I had a VERY dominant dog and should be careful.
In the first few months we had him, he snapped a lot at us and one time when he got into some food that we were about to eat, when we went to correct him (tell him to "leave it and go to his crate for a treat) He lunged at me and between my fianc