It sounds to me like a case of poor early socialization. Yes, he was abused, but out of ignorance. What puppies aren't exposed to between 6-12 weeks, they may fear all their lives. This is tough to work around. You can see that couple didn't manage to do much in a year. What you need to do is go right up to what ever he is afraid of and pat it and talk to it in a happy voice. ''Good vacuum cleaner, what a good vacuum cleaner.'' I did not choose to do that with my one puppy that was afraid of ladies in broom stick skirts.
Work at building his confidence. Start with obedience training. The key to most behavior problems is approaching things using the dog's natural instincts. Dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog. Life is much easier if the 2 legged pack members outrank the 4 legged ones. You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at
http://www.dogsbestfriend.com/ As you praise the dog for following your commands, it will build its confidence.
Play tug of war with the dog and lose. However at the end of the game, take the rope or toy and put it up, less the dog becomes confused about who is top dog. Ropes from the pets' store quickly turn to hazardous shreds. Ones I made lasted much better. Go to a hardware or home center that sells rope by the foot. Buy 2' of 3/4" poly rope. Melt the ends, and tie knots in it. Get them as tight as possible, put it in a vise and pound it with a hammer. Watch carefully, and be ready to discard when it comes apart.
Finally, make sure it has a den to live in. If you are not using a crate, buy one. The dog may be happier in its den than loose in the house. It relaxes, it feels safe in its den. It rests, the body slows down reducing the need for water and relieving its self. Dogs that have been crated all along do very well. Many of them will rest in their crates even when the door is open. I think the plastic ones give the dog more of a safe, enclosed den feeling. Metal ones can be put in a corner or covered with something the dog can't pull in and chew. Select a crate just big enough for the full grown dog to stretch out in.
A dog that has not been crated since it was little, may take some work.
Start just putting its toys and treats in the crate. Praise it for going
in. Feed it in the crate. This is also an easy way to maintain order at
Feeding time for more than one dog.