dkm1987 is more qualified than I am to cite scientific sources so I will leave that to him. Let me address some of your specific issues;
"Pre-existing Concepts that HST Refutes:
* A muscle must be fully recovered before you should train it again.
* You should not train a muscle that is sore (DOMS, not injury).
* You must never train a muscle on consecutive days (i.e. train the same muscle everyday)."
Yes, HST refutes the above but only because science has shown recently that those old notions are, in fact, incorrect. I will let somebody else give you specific references since I do not personally catalog them.
"* The concept of "Overtraining" in general as it applies to bodybuilding.
* You must train with maximum "intensity" to elicit significant muscle growth." (That is true when you are talking about a conditioned muscle, i.e. one that has become accustomed to a given weight or hit its point of repeated bout effect. However, HST allows for the DEconditioning of the muscle so that a maximal effort is not necessary to achieve maximum results).
"* You should not use eccentric training on a "frequent" basis." ( Science has shown that eccentrics have no significant impact on the nervous system and, therefore, will not lead to overtraining. Concentrics, on the other hand, require the use of neural strength which can lead to overtraining. HST tries to walk a fine line between concentric and eccentric movements and maximizes the anabolic period for HYPERTROPHY by extending the total workout time bewteen deconditioning through the use of eccentic reps.)
"* You must change your exercise selection regularly in order to "confuse the muscle" into continued growth." ( I agree somewhat with this statement. In fact, I no longer believe that, for hypertrophy, multiple sets are an efficient way to grow muscles. Variety, I believe, is key. Bryan, I believe, disagrees with me on this point but that is really notrelevant to HST anyway).
"* You must hit a muscle at every angle in order to adequately train it." (Same answer as above).
"* Muscle Fatigue is the primary indicator of having triggered the growth signal." ( Again, many scientific studies have shown that fatigue is not necessary for growth, Of course, you can grow with fatigue but why put in all that extra work when less sets will provide the same results. Also, HST relies on recent studies that show that frequency is more important for HYPERTROPHY than volume. However, if you combine high volume with high frequency, you will likely end up overtraining. They are not compatible).
"* You must effectively isolate a muscle in order to train it effectively." ( Actually I am surprised to hear a powerlifter say that. I have never seen a powerlifter doing dumbell tricep kickbacks. To me and, I believe, most power lifters, complex movements are superior to isolation movements).
"* You can train a muscle in such as way as to change its natural shape." (Tell that to my legs! You can make a muscle grow which will impact its shape. However, A person who does not have the genetics to allow for a peaked and split bicep is never going to have one, no matter what Weider and some other 'for profits' gurus say).
Hopefully one of our more informed science collectors will come along and give you some specific references to refer to. Mine is the condensed, non-technical version.