Bless you for wanting to help this pup. Although he may be truly feral, he may also still be somewhat traumatized by the whole experience of being caught, put on a plane, driven to a noisy shelter, then taken to another unfamiliar place. For now, the best thing you can do is not try to engage your dog (hard as that is!). Leave him space to observe you, don't look at him directly. Imagine if you were in a room with a lion. Anytime the lion approached you, your first instinct would be to run. But if the lion completely ignored you and didn't seem to know you existed, you would gradually get braver.
Routine is also very important for fearful dogs. Feedings at the same time every day. Is he using potty pads? (I'm guessing you can't take him outside to potty) Clean the area up at the same time every day. If you have to do something scary (grind coffee, vaccum) try to do it at a regular time. The more predictable life is, the less frightening it becomes.
Here's are some web posts: article from Best Friends about fearful/feral dogs; tips on how to behave around shy dogs. This website is from a trainer who works with fearful dogs. Definitely look for a trainer in your area who has worked with very shy dogs. He or she can offer many useful ideas and tips, especially in the area of body language.
Good luck! Your pup will improve, although it will takes lots of patience and acceptance.
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