I have personal experience living with a dog that was raised (with his 8 littermates) by his dam, in the woods until they were about 5-6 months old. The dam was an escaped sled dog, and she went to a woman who had a nearby cabin for food, for several months, before anyone even knew there were puppies.
I will preface my personal experience with the very strong sentiment that every dog is different. Breed, life experience and temperament are going to shape the dog. The dog I am speaking about was a husky-type, male dog with a fair amount of rank drive (desire to move up in the pack), and an EXTREME prey drive.
When I first got him, he was not really that shy, as he had been with a foster for about 2 weeks, and was pretty food driven. He was extremely destructive, and extremely prey driven - for real prey (such as my cats, snakes, birds - he caught several out of the air, rodents, etc).
At the time, I was actually working as a dog walker, so I had him with me all the time. In quick order, I learned that he was a MASTER escape artist. He would actually stay close to me on the walks, but if I tried to leave him crated in the truck, he would be out of that crate in no time. I have a rather humorous story about how he busted out of the crate, and chewed on the horn so that it was a continuous honk all the way to the mechanic... and oh, he has also chewed through my seatbelt. I also have a rather not-humorous story about how he broke out of his crate, knocked down the bedroom door, pushed out the window a/c unit, jumped out the window, scaled the fence and killed my neighbour's cat.
But, I'm getting off topic here. Ultimately, he was a wild dog. I lived in a city at the time, and city life was not meant to be for him. His destructive nature only got worse with time, he developed some separation anxiety I think, and he simply could not be crated (I could physically crate him in a plastic crate inside a wire crate with locks on it, but he would injure himself trying to get out).
Of course, looking back, there were things I did wrong. I let things go for too long, thinking he would come around, and things got worse. He adapted his wild dog ways to my house - which was destroyed.
While you do need to build up trust, I would caution against coddling a dog like this. I would say that a very, very strict routine would make her feel secure. I also would not leave her alone at your store just because you can't get a leash on her. She is essentially still living as a stray dog with you as a food supply, occasionally throwing a blanket over her. Since she follows you around, I would try and get a collar on her, and tether her to you (tie a rope to her collar, and the other end to your waist). Then don't approach her or go after her, just go about your business and she will have to follow you. Carry lots of yummy food items with you, and reward her when she sits beside you or looks up at you (marker training as mentioned above).
Have you tried to crate her? I would guess not. I would start out by just having a crate available to her, and leaving the door open. If she is truly a wild dog, she might take a while to be ok with being closed in the crate. But, if she is that timid, she might enjoy the solitude - you'll never know until you try.
The longer you go letting her live in your shop, peeing on paper, the more enforced it will become. If you are serious about this dog, and don't want to live with a wild dog, you will have to take some steps.