Great for you for taking the dog in!
What he really needs right now is a combination of love, tenderness, and discipline/routine. Not discipline like "No, bad dog!" but making sure you're the one calling the shots - if you're asking him to do something you don't necessarily need a "stern" tone, you can give him commands with a happy voice too! It is important that he have boundaries, though, both to establish his place in the household and to help him learn to trust you. That's one reason NILIF is so, so helpful - when a dog knows what's expected of him he gains confidence and becomes less fearful. Meanwhile you get a very well-behaved dog who's happy to do what you want - everyone wins :)
Because this is such a delicate situation and there is the potential for you to get hurt, I think it's a very very good idea to follow the other posters' advice and find an animal behaviorist to come help you learn what to do. You'd be amazed how much many abused dogs can "recover" with the right training!
Here's a couple of places to get started looking for behaviorists (though do call the shelter and your veterinarian for recommendations, too):
http://www.iaabc.org/consultant_locator_dogs.htm
http://www.apdt.com/po/ts/us.asp
Other places you might look (I personally have never used these, though, so I'm not sure how helpful they might be):
http://www.animalbehavior.org/ABSAppliedBehavior/caab-directory
http://www.geocities.com/l_herf/behavior.htm