If you haven't already, I'd highly suggest pausing your new video just at moments where your entire body is in view and just prior to your release. For instance, pause at the 3:27 mark where the ball is locked and loaded above your head. I think this mark (and the 3:55 point) both serve as great places to begin a breakdown of one's own shooting stroke.
From that freeze-frame:
1. Take a look at your feet:
They're pointed nearly 45 degrees away from your target (the rim). Further, your right foot seems at least slightly too far in front of your left foot; the effects of which are likely compounded by the aforementioned lack of squaring to the target.
You mentioned how you could not get your right knee to stop crooking. I believe that crook is almost entirely a result of your feet pointing in the wrong direction combined with the right being so far in front of the left. If you just stand around like that in real life while you're randomly waiting in line at the grocery or something, with your feet all staggered and crooked, at least one of your knees would probably have to bend a funny way to compensate, yes?
Often, when our shooting stroke is running amok, we tend to look at our arm mechanics as the primary culprit. And in your case, I do think there's some arm motions we could work on (which I'll refer to later). But I think every shot must begin with a solid base, meaning from our feet on upward. This means squaring your feet to the basket every single time you shoot.
Force your feet and check your feet (or have a friend check them) to make sure they're square (aka pointed at the basket) every time you shoot. Once the correct squaring process has been established, this will likely throw off the rest of your stroke temporarily, since your body is accustomed to attempting to score while crooked.
Further, it is likely going to help to maintain a wide base as you begin working toward squaring the feet. A wide base will centralize your balance and simplify the shooting process. The closer our feet are to one another, the more likely it is for us to experience a slight balance shift when attempting to shoot off the move, thus leading to an inaccurate shot.
2. Take a look at your knees/body:
I recall feeling as though I was exploding on my jumpshots at one point, only to realize - once I watched a video of myself - that I was actually nearly standing straight up during the entire process. That's what I'm seeing here. You bend your knees slightly during the shooting process, but in the scheme of things, its effect on your stroke is negligible.
If you still have your screen paused around the 3:27 mark, I say rewind it a few seconds and re-watch your shot in full. Can you notice the lack of legs? It's nearly a standing-straight-up jumpshot. Being so upright will often result in a slower, less explosive, less powerful, and ultimately less effective jump shot.
With that said, merely shooting around with oneself is often a breeding ground for bad habits and the first thing that tends to hit the shelf is the legs. But it's important to remind oneself to implement them at all times. In your case, I'd suggest bending your knees before you even catch the rock (perhaps acting like you're coming off a screen), so it feels as though you're crouching. Work on catching and squaring one's feet while staying in the crouch position. Its then simply a matter of exploding upward for your shot. This leads to. . .
3. Make your stroke one continuous motion:
I think largely a result of your crooked base and lack of leg power, you seem to have compensated with a healthy catapult motion. By this I mean, your shooting motion often seemed to consist of raising the ball upward, cocking it back, sitting in a pocket for a moment's notice, before finally moving forward to complete the stroke. Again, I'm using 3:25 as an example. It's part catapult, part fling.
Here's an example of what I think we should shoot for: http://www.youtube.com/watch?v=PzLA78Qb3fg#t=1m25s
Take notice of how Hamilton is already low with knees bent. He's not all-out in a crouch, but he's surely not straight up. Once Hamilton catches, next take notice of how his shot rises and releases in one continuous motion. Then compare that to your shot which seems to rise, head backward for a moment, freeze, then proceed forward. That's what we want to try to eliminate. Looking at your old shooting video, it doesn't look like that catapult was always there. It's as if someone told you your shooting pocket was too far in front of your body (and it may have been) so you went in the complete opposite direction.
In all honesty, I think fixing up the legs (squaring them/using them) may eliminate some of the catapult tendencies naturally. But I still think it's going to help to work on some one hand shooting (that is, standing close to the basket and practicing using one's legs and only the shooting hand to rise and follow throw in one smooth motion).
I'll say, your arm motion is already a lot of the ways there. It changed throughout your new video as you took instruction it seemed. For instance, many times you'd seem to snap your shot, then a moment later, you'd display a pretty solid follow through. But for all intensive purposes, your arms are largely on the right track (as long as that follow through becomes consistent and the catapult lessons).
Essentially, I'd recommend practice and repetition. With my brothers and players, that often mean we "shoot some shots", which is our way of saying we partner shoot. One person shoots and gets his own rebound, then passes to his partner who should be squared up or pretending to come off of a screen. We often shoot in groups of 50 makes. It's a good way of working on shooting fundamentals without having to shoot, rebound, dribble slowly back to a spot, shoot again, etc.
Work on creating one fluid upward motion. Start low. Square feet. Wide stance. Rise and release with the legs.