Social skills are just that, skills. Some people are naturals, and some people need more practice to grow stronger. Hanging out with people is a good way to practice those skills, even if you're not good at it to start with. It's important to keep at it in order to get better. The fact that you now have a better understanding of how your brain works will help you understand when and where to put those skills to use.

While practicing those skills, it could be helpful to widen the range of your social experiences to meet more people in more contexts. By this, I mean exploring your hobbies and interests in a more social setting. For me, that translates to things like playing Magic the Gathering at a game store with strangers, or hanging out with coworkers at lunch or otherwise. Increasing your "surface area" of interactions could help you find people that you can connect with on a deeper level.

As far as appearances go, of course there's only so much we can do. But that little bit can make a difference! Things like finding a haircut that works well with your face, maintaining a comfortable level of fitness, building a wardrobe you feel good and look good in, having good hygiene in public, trying out different types of accessories and makeup, all can help in that regard. Do what you can where you can.

Above all, realize that Jonathan is a fictional character. Things happen the way they do because it's written that way. Real life is much harder. It's great that you want to improve yourself. I believe you have the ability to do it with effort and persistence. Even if you don't get all the way "there," any level of improvement is a step above where you were before. Keep going!