My husband and I went to high school together and started dating long distance while we were in college. And oh, boy, do long distance relationships come with their own unique problems (in addition to all the normal problems of close proximity relationships).
Was this the first visit you two had since you started dating? How far apart are you two?
I don't think you've ruined things at all. I do think you need to try to talk to him, and let him know what's going on in your head and how you're feeling. Communication is important in any relationship, but becomes even more important in long distance relationships because, quite frankly, that's all you have 90% of the time. I would probably start by telling him how much you enjoyed the weekend, and you're sorry that you got a little clingy/smother-y at the end (if that's how you truly feel). I think it's perfectly fine to say to him what you said here on the forums.
I agree that you do need to give this relationship time to grow and try not to stress too much (easier said than done). Keep up with your own activities and stay involved with friends and hobbies. Don't let yourself focus on him 100% when he's not there.
I think it's a little early to have the talk about ending the distance, but have you thought about it at all?
I'm sorry if that wasn't much help. I really think you do have a good handle on the situation, so I don't think you need to freak out or anything. Just start building communication and trust, and you'll get there. You also need to build some trust in yourself. There's nothing wrong with going to a therapist to get some help building self confidence and learning to feel better about yourself. Try to acknowledge when you're having irrational thoughts, and replace them with rational ones.
Good luck!

Feel free to PM me if you want to talk more about this!