While I appreciate how protective of him you are, I think you need to detach yourself from him past. Yes, he didn't come from the best situation but he's no longer there -you got him out. I feel like you're still feeling so sorry for him because of where he came from and, while this is a nice thought, it's not really productive.
I can guarantee you, he doesn't remember his past. All he knows is whats going on now. You hanging on to that past isn't helping anything, in fact, it could be getting in the way of better judgement. The fact of the matter is that he needs one of two things right now: he either needs medication or he needs to be introduced to some friends.
Maybe I'm wrong, but it seems to me that you've already made up your mind that you're not going to introduce him to friends. If you're thinking that keeping him alone is going to help his shyness, I think you should know that that's not how it's going to work. Quite the opposite, actually. He may not know it, but he
needs the companionship of his own kind. He panics because he'd probably never seen another rat before your first intro attempt. Of course meeting something new for the first time would be exciting (either in a good or bad way) for him. He's probably gravitating to you because he's sensing that you feel sorry for him and he's taking advantage of that. He doesn't
want to meet new friends, so he's going to you because he know that you won't make him do it again.
This means, as long as his health really is fine, that it's time for some tough love. We, as the humans, take care of our pets even if they don't always like how we do things (For example, my dog hates getting her needles. She cries like she's being killed and the first time she did that it really bothered me. However, I knew it had to be done so she has never missed a vaccination. And, honestly, she completely forgets about the needles as soon as they're finished lol) We
know that it's unnatural and mentally unhealthy for a rat to be alone...he doesn't. You have to show him how much better life is with friends. It will take time, but in the long run it's the right thing to do and he will be much happier that way.
I'm not trying to pick on you, and neither is anybody else. We all know what it's like to take in these animals who have had such miserable lives and all we want to do is make them happy. And that's great but we have to remember that the animal's well being has to come first. Once that's out of the way, then they have a whole lifetime to be spoiled
