I found a puppy in a ditch 4 years ago. She was the most terror-stricken dog I've ever laid eyes on. The vet pointed out some signs of former abuse on her you wouldn't want to hear about. She was not a candidate for adoption. I couldn't even bathe her without her screaming and rolling her eyes, fighting, etc. Two things that worked best for us in helping Bingo, as we named her, were tons of lavish praise, & the efforts of our Lab, who mothered Bingo & patiently taught her to play & smile again.
If you can find one or 2 things your timid dog does well that you can praise him for, I would load on the praise every single day & make a great big fuss. One thing Bingo does now is go & get her collar every morning & bring it to one of us. Sometimes she does it before we tell her to. Her big eyes are happy & expectant because she knows she will get a full minute or 2 of total praise & positive attention, just for her. Praise also got her to accept being bathed (after about 18 months of giving it). Today she will jump into the tub for her bath when I tell her to. She is not the same dog at all, & those 2 things are what did it for us. I hope Bingo's story might be of some help to you.