How to untrain a dog/Seperation anxiety ??

We got our new dog, and he is the best behaved dog. Ever. He has to learn commands and tricks, but he has very very good manners and etiquette. He won't step through a doorway without permission, has a perfect recall, and knows not to beg. A problem, though, that I have with his training, is that he needs permission to eat and drink. I have to put the food in his face and say "Eat, good boy," and after after every bite or drink he has to have reassurance to continue. He really won't eat more than three bites or so without refusing to eat. I think he is pretty underweight how it is, so I need tips on untraining him from this.
Also, he had severe seperation anxiety. Just from me, and I'm not being vain. Even if he is with someone else, he will whine and try to follow me where ever I go. This is a problem because we have to keep him seperate from our other dog (we're working on this), and now I have to crate him just so I can go downstairs. We had the stairs blocked with a gate, but he has learned how to open that. He is not even scared of his crate, he just doesn't want to be away from me.
The seperation anxiety is going to cause some real problems, since I am on summer vacation and am able to be home with him all day now, but when I start school in the fall, he will have to be crated for three hours at a time (my dad will let him out at noon)
One more problem. It's pretty simple, I just need to ask if I'm going at it the right way. He has a fear of men, and will run away from them if they approach him. I am asking men to feed him treats when they meet him. I hope this is right.
Thanks.