I am not sure if this is a "Who is right?" situation. The fact that you ask that question is a clear statement about you and how you handle conflict.
I am a person who has long-term male friendships. I am a careful opposite gender friend and I am very transparent with my partner and the partners of my friends.
But you are not comfortable with this friend and you haven't been from the beginning. You aren't going to look upon anything she does in a favorable light. She could be Mother Theresa and you would still have a problem with her.
Let's go though your list:
1.) BF problem. She was polite to you and then pigeonholed your bf. If he was a good date, he would have extracted himself from her and returned to you.
2.) He *is* her best friend. Not everyone feels that their romantic partner should fill the roll of best friend.
3.) As her best friend, when she had a spare ticket to a concert, she invited him. She is not required to sell the tickets to both of you. If your BF didn't want to go, he should say no. Again, she isn't your problem, your boyfriend is.
4.) Unless the cupcakes said "I love you with all of my heart", they were just extra cupcakes. If she brought a bunch, I am assuming that she wasn't expecting him to eat them all himself. Since you know about them, did he bring them home and share them with you?
5.) And your answer can be "No thank you, I don't want to be a proxy in your wedding. We will just come and dance the night away!"
5.) Again, you can say "No thanks, we would rather be alone on Valentine's Day. I am sure you understand."
6.) You do know him better in some respects and she may know him better in others. There is a certain body of knowledge that comes from knowing someone for years. That comment wasn't an insult, it was an acknowledgement of your primacy in his life.
Your examples are not strong ones of her intruding on your relationship or of her having designs on your boyfriend. If those are the best ones you can come up with (the Valentine's examples are almost a year old), my opinion is that you are too sensitive and are not comfortable with your boyfriend having a close female friend. If that is the case, you need to be honest with yourself and your BF. It sounds as if you want him to cut her out of his life.
Personally, I have watched guy friends drop any friend with a set of ovaries when they get a new girl and then -- lo and behold -- they are back in a couple of months to a year sheepishly apologizing for giving into the psycho-chick who wanted to run their lives completely.