I have a 16 year old daughter too, and part of it is the age. But, you are still the parent. never forget that. The rational part of their brain is not fully developed until they are in their 20's, so YOU have to guide them.
First off - does she have a cell phone? Do you have possession of it at night? Kids think NOTHING of 2 AM phone calls. I suggest when you go to bed, the house phone and cell phone go to your room with you. Read her texts. (I know I'll get blasted for that - kids earn the right to privacy, it isn't automatic, and she doesn't sound like she's earned it)
Secondly - does she have unlimited internet access? No teen needs a computer with internet in their room. Password your computer and shut it off when you go to bed. If you are brave enough - put a keystroke recorder on it.
Does she have a job? Do you ever randomly check to make sure she is there? Does she have a car? If so, do you have the keys at night so she isn't making late night visits anywhere? Do you ever check to make sure she is where she says she is? We do - and it only takes ONE time of catching them for them to quit sneaking around. We rarely even check anymore because she knows we check. When she goes to a friend's house do you call the parents, and go to the door to make sure they are being supervised?
As far as the boy goes. To forbid it is to make it more enticing. I personally would just make it as tough as possible. Set high standards to enable her to go out. Like "you can go if your grades are all brought up to 78" - or "if your room is clean, your chores done, your homework done, and your laundry done". Make her work for it. That, combined with limited cell phone and internet access may be enough to make it not worth it, or at least run it's course fast. Oh, and of course, invite that boy over, make him and her sit in the living room with the family, play a game of cards, interact. If his motive for seeing her is not good, he'll HATE that, and move on to his next target very quickly.