First off, you're NOT a loser. You are obviously a well-read, literate person with a great deal of intelligence. Being "scrawny" is a great thing - one heck of a lot better than being overweight. And you're tall; the average height of a man is 5'7"! I am a 5'9" woman married to a 5'7" man, so don't give up!
As for your acne, I know of people who have had great success with products like Proactiv. Or talk to your regular MD - or a friend - to find the name of a good dermotologist, and go see him/her for medication to treat the acne. Acne is mostly determined by heredity, although few people make it through the teen years without getting afflicted.
It's killing you to see your best friend and your best female friend together. Stop. There's no point in continuing to torture yourself. So make plans to see your female friend and tell her how you feel. Like you said, she should know! If she was flirting with you early on, it could be that she harbors hidden feelings for you as well.
Just remember that she IS part of a "happy couple", and so be ready to lose that friendship one way or another. Tell her your feelings, or not, but STOP with the self-torture. Work on finding a job, getting your own place, and get started on your own adult life. Once you're in the workplace, you're going to meet a lot of people, and you never know which one might be "the one."
You'll also be able to find more male friends. Just remember to treat people with friendliness and sensitivity, just as you want to be treated, and you'll have no problem finding someone. Remember that when you go out on a first date, try to listen more than you talk, and ask the girl questions about her school years, her family, how she gets along with her sisters or whatever. There are tons of topics, and once you're out there, you're going to find the world is a BIG place with LOTS of people who are looking for a friendly face in the crowds.
As for being a virgin, be honest with your girl, when the time comes. Ask her to, well, teach you (but in a way that doesn't make her sound slutty!). It's actually a big turn-on to find out one's date is a virgin when it comes to be time for love-making. Just don't be too eager -- that's a HUGE turn-off for women. And remember - you're going to make someone a great husband and even father, someday! You are obviously intelligent, so don't waste any more time with this current situation! You're in NYC, dude! Get out there, get a job, and meet some people. I KNOW the right girl is just waiting for you!