roger is exactly right. you want the hyperextension of the back (sometimes called getting a "c" with your lower back to transfer the momentum generated from the lower body through the trunk and into the shoulder. pedro martinez can really get to this position. there is an excellent video clip in latin superstars showing him almost directly from the side. this requires your shoulders to be behind or at least verticle at foot strike. clemens looks like his shoulder is in front of his hips at leg pump but then he agressively pendulums his hips in front of his shoulders which is phenomenal. if your shoulders are in front of your midline (belly button) at footstrike you are going into rotation too early and losing some leverage and velocity by failing to time the transfer of force you develop in your lower body pushing against the rubber and driving force into your hips. no way you can get maximum hip and shoulder separation.
if you break the kinetic chain running from your back foot to your throwing hand fingertips, your arm takes over and the small muscles tire quickly. this is where many pitchers lose velocity or get hurt and why some pitchers can throw 50 pitches and go down, and some guys can throw 110 pitches with no problem. the farther your shoulders are behind the hips, the farther you have to accelerate the ball using the big muscles by separation of the hips and shoulders stretching and activating the big muscles of the core if you time it properly. this takes great strength and flexibility to do 100 times in an outing and why developing core strength and flexibility are critical to maintaining a healthy, high velocity fastball. you should see the core workout my 15 yr old does 3 times per week. it's tough.
there is a great clip of nolan ryan from behind doing this on one of the other threads on this site. as he pumps his stride leg up (extremely high), when it gets to the top, the first move is to get the hips going toward the plate and the upper body lags behind. then he keeps an excellent angle from his head/shoulders to his stride foot as he breaks from the glove and continues down the mound. notice how he keeps about 90" of flex in his elbow as it comes up to the high cock position. he never extends it behind him.
he starts to rotate and square to the plate just before foot plant but he has plenty of room left to rotate and square the shoulders up to release the ball way out in front of his head. his front leg does straighten and lock out momentarily but that happens immediately after he releases the ball, then he continues toward the plate with his head down. he watches the pitch with his head below his waist.
the hand then comes to rest on the glove hand side of the body loose and with plenty of time and room to decellerate and cushion the elbow. if the throwing hand stays in front of you it sends force and a shock back to the arm and shoulder instead of the large muscles of the back.
then the other plane you can use is rotating away from the plate (showing your back to the hitter) to get more leverage and torque. you must be careful here because excessive counter rotation (like kevin brown) is hard to control and if mistimed, can place pressure on the throwing arm. big payoff but a big gamble.
a good way to practice late rotation is to place the stride foot in a chair or on top of a weighted 5 gallon bucket about 3/4 of your stride length toward the plate (3/4 of your height, i advocate striving for a stride length as long as your height or more). your back foot is wedged against the rubber ready to push, and your throwing hand is in the glove preparing to break (not separated with elbows up). i think you need to feel the critical timing of the lower body and hand break to keep the kinetic chain and momentum moving through the body properly.
you then count "1" placing your weight on the front foot on the bucket or chair, "2" shift your weight against the back foot slightly lifting your stride foot off the bucket/chair (someone must move the chair out of the way quickly when you do this so you do not alter your finish, and "3" break the hands and push off the rubber staying sideways (or closed) as long as possible moving toward the plate and getting the throwing hand into position behing the head (some people call this short arming and a bad thing but we'll talk about that in another post). then stride the length of your body and throw the ball finishing with your head below your waist and you should be in pretty good position. it's easier to explain with a video clip. i'll have to try to upload one sometime.
try it, it's one of the first lessons i do with a rookie pitcher after backward chaining to feel release in front of the body and then throwing with a running start.
this is turning into a dissertation, hope you didn't doze off.