My dog also has pretty bad seperation anxiety with her when I leave have a bit of a routine that helps her becuase of her insecurity, I take her out for a little short walk in the morning then take her down to where her 'play pen' is and leave her there but i dont make a big deal about it, no talking and hardly any touching. I just leave her, but when I first started I did the thing where I would occasionally open the door and see her so she would know I would be coming back and increase the time I left her alone so it wouldn't be that big of a deal. But when I'm off to somewhere for a long time she tends to stick to my mom or hide in my room. when ever some one touches her or tries to pick her up she bites them and looks for me, or so I've been told. She's getting better but only going to take some time before she gets over her fear.
As for crate training I would either do what criosphynx said or try a playpen type thing, its basically an exercise pen with things to keep the dog preoccupied while you're gone. I am not allowed to keep my dog in a crate all day because of her past therefore the rescue allowed the idea of a play pen for her and it is great she doesnt seem to mind going in the pen versus her crate which she for the most part hates unless she is scared or nervous. Try putting a crate in there with something of you're scent so he can go in there and basically have your scent and reassurance when he's in there since he's attached to you. and start off in a place where he can see you such as in the kitchen or living room.