Being collar/head shy is not all that uncommon, even in dogs who weren't abused. When you grab for a dog's neck, instinct tells them to defend themselves sometimes, because in the dog world that can be an attack. I think what often happens is they come to associate being grabbed by the collar as something unpleasant. Tommy used to cower and flop down and just generally panic when I reached for his collar. I'd be careful and never grab the dog's collar when you are angry or emotional in any way. For one, you were probably irritated that he hadn't gone downstairs, so he sensed that tension. That, on top of grabbing for his neck (in his view), made him feel he needed to defend himself by mouthing your arm. I don't think it's necessarily aggression, but a defensive response. If someone walked up to you obviously angry or irritated and reached for your neck, more than likely you'd want to push them away too .

So as has been recommended already, if you need to lead him somewhere I'd suggest a leash. I got a slip lead to use for Tommy, so that I could just slip it over his head and then he'd get right up and follow me. Try to never approach him and take his collar while tense/angry/irritated. Meanwhile when he is relaxed, handle his collar and neck area a lot. Take a hold of it and then let go again while petting him often, so he comes to associate it as a routine thing that's no big deal, and not something that's going to end up with him being pulled somewhere.

Classes are good too, they always strengthen the bond between you and allow him to see you as leader. I don't know how treat motivated he is, but try to encourage him often to come to you for treats. Treat him every time he comes when called for now, and even if he gets it down and starts coming well, be generous in rewarding him for it. It's the most important command there is, in my opinion.

I hope some of this helps you.

*Edited to add: Some of this is a repeat of the advice Glacier gave, we were posting at about the same time, I definitely agree with her post.