I'd be glad to go into detail for any questions you have.
It seems that starving and binging is the most unhealthy thing you're doing right now. It can really mess up your hormones!
I'll share an anecdote: I knew someone who went to the doctor for a case of, for lack of a more technical term, "man-boobs." He was worried, rightly so, about his hormones. The doctor did some tests and told him he had the hormonal profile of a prisoner of war; sometimes, he said, when soldiers are taken prisoner and starved in death camps, after they come back to their home countries and finally start eating again, they gain fat in weird places. It sounded like he destroyed his testosterone production and maybe gained some estrogen. The doctor said this often happens to people with bulimic eating habits. When i first heard this, i was like, "There's no way you're bulimic, you don't throw up your food!" But apparently, according to the doctor, bulimia refers to going for long periods without food and then eating a huge meal to make up for it. Sure enough, my friend had been eating, at most, one meal a day.
Anyway, the point i was making is that these eating habits can screw up hormones so badly, they can give a man boobs. Nobody probably notices it on girls though, because we're supposed to have boobs! But an excess of estrogen can mess us up too, because it encourages fat storage and discourages muscle.
So it's really important to space your food out throughout the day. Usually, i boil up a giant pot of lentils in the morning or whatever so i can munch on the rest throughout the day. It sounds like you have the right calorie amounts, you just need to split them up more and you should be fine.
About the squats:
Sounds like you have a case of crunchy knees. My left elbow crunches like the soundtrack of a mortal kombat movie whenever i curl or bench press, and it burns like crazy! Only my right knee has started crunching lately, and only when i'm careless about it. Still, i think this advice can still apply.
When i was in physical therapy, they would heat up my elbow with a hot pad before my exercises. They would also use an ultrasound machine, they said it encouraged blood flow to the area. The heat and ultrasound would loosen up the joint, sometimes almost to the point where it wouldn't crunch anymore! It was after all this that they had me do exercises with it. After the exercises were done, they would chill it with an
ice pack, to reduce swelling and inflammation caused by the exercise. After i could no longer see a physical therapist, i've tried to duplicate the physical therapy experience. Obviously, i can't afford an ultrasound machine! But i did get this handy reusable gel pack that can be heated up in the microwave or tossed in the freezer.
You can probably make the same kind of heat pack with a towel or washcloth soaked in hot water. When the towel starts cooling down, dip it in hot water again or toss it in the microwave. Just be careful not to burn the skin! Before i got the gel pack, sometimes i would fill up the bathroom sink with hot water and just stick my elbow in it for 20 minutes or so! That might be kind of awkward to do with knees, so maybe just stick with the hot towel. If it's too wet or messy, maybe you can do it over a bathtub. A hot bath might work well too, it'd heat up your whole body in that way though, so you might come out looking like a lobster, lol! Anyway, once the joints are heated up, they should feel much looser and crunch less, so that's the perfect time to exercise. They may still crunch during strength training, but it's better than crunching without strength training; it can only improve their condition. Also, after your workout, you'll be soothing the joint with a cold compress. This can be done easily with a plastic bag of ice cubes, add a little bit of water so that the bag will conform to the shape of your knees. Like with the hot towel, be careful not to damage your skin; i usually wrapped my ice bag in a t-shirt or towel.
Another thing about squats is that form is VERY important! Be sure your knees point in the same direction as your toes and keep your lower back arched. When i started, i studied the hell outta stuff like this:
Barbell Squat Lurn 2 squat good -- E-ZY! From dork to diva
Basically anything in the training section of stumptuous is good. Exrx.net is also a great resource for form, anatomy, and medical stuff in general. If squatting still makes you uncomfortable, you can try the lunges and split squats listed here:
Thigh Exercise Menu and just substitute "dumbbell" with "milk jugs" or whatever.
Hope that helps!
Brolic chicks are harder to kidnap! 
