Obedience training is great for confidence. I've also had great results with some agility training - basically a half sized ramp and some small jumps. One of our dogs was so depressed at the shelter she would just drop on her back and pee whenever anyone came up to her. Basic obedience helped, but the agility ramp was magic item for her confidence. She's an extremely happy and confident girl now (next month will be her 4 year anniversary of joining our family.)
In 2001 we had three "little" Australian Shepards come into the shelter here. They were all apx 5 months old and were clearly feral. I spoke with one of the professors for the NC State Vet School and, along with a vet student that wanted to be involved, we worked out a simple study to compare rehab methods. While there are lots of opinions and claims, there is essentially no valid data to support any approach over another. Unfortunately, the males demonstrated some rather aggressive tendencies and the decision was made to euthanize him for safety reasons. One female went home with the vet student who had specific instructions about her approach. She was to use a "hands on" approach which forced contact on the dog, though in a positive way. She would handle the dog, wrap her in a blanket and hold her, etc. I brought the other little girl home planning to use a more passive approach, using treats and praise to try to bring her along. Unfortunately the other girl, Fanny, became very ill and didn't make it. My little girl, Bonnie, is doing well over two years later, but still has a ways to go. Personally, I believe the more aggressive approach may have worked better, but we had to abandon the study since the other dog died so soon. Bonnie has a home for life, so there's no issue there, and continues to make slow progress. Here's a more complete story of Bonnie, though I'm behind on updates: http://www.dogsled.net/rescue_of_bonnie.htm
There's nothing quite like rescuing either a dog or a cat. You have done a wonderful thing bringing this dog into your family. Siberians are one of the most frequently surrendered breeds, and have a rather low adoption rate from shelters (for the same reasons they are surrendered - high activity level, need lots of attention, shedding) I am very touched with every one that gets a new home. Thank you for sharing this with us.