I've sorta been following the story love, and I do think you might need to consult another adult in the matter. If it is this bad, there may be a chance it will escalate. Now, I don't know this guy like you know him, but again, bullying is bullying, no matter what.
And honestly? As a person who's been a victim of bullying myself, I feel this guy is being unbelievably petty. I understand there was some rift between you two in the past, but you were willing to step up and accept your fault. That takes a lot of courage and growth to do. He doesn't have to forgive you, no, but him going out of his way to purposefully make you uncomfortable when you've apologized and meant it and have not done anything to him since...that's very petty and unhealthy behavior. In fact, it makes him a hypocrite -- why give back the treatment you were given (or at least something similar)?
I've been a victim, but I moved passed it. I didn't forgive my bully, but I didn't go out of my way to be spiteful because I just had other things to worry about. And I certainly never felt the need to bully them or anyone else for that matter. Maybe he's not passed whatever when down between you, but he should handle himself much better.
I think going to an adult, someone you trust, needs to happen. Because this is affecting your ability to function in your class, and that can affect your ability to perform there as well. And I feel your counselor believed in him because you went to her and he wasn't there. So she most likely went to him with what YOU said and he did some "oh, it's just a misunderstanding".
So you might need to sit down, the both of you, and talk it out with an adult ( if not more -- like your parents). Because this can't and shouldn't, continue. His attitude shouldn't continue like this because it actually makes me wonder how he's like with other people or how he could potentially be like.
These are my two cents, and you shouldn't rush if you're still uncomfortable. But please -- make sure you have people around you to support you and work with you through this. This is not something you should endure just because "I did wrong in the past, so this is what I deserve". You also owned up to it, and meant it with your heart. If he can't recognize that, that's his problem.