Mitch and Troy make great points and arguments.  I agree in part and dissent in part.

 To Mitch’s argument:  Stephens does count in his interpretation of the Confederacy being its first elected VP, just as much as Cheney counts in his official rhetoric as to the policy of the US Government today.  My point was the to use the late Stephens as to somehow  downplay the reason for the War is disingenuous and incomplete (I think you agreed with that part).  The Lost Cause thesis was crafted after the South’s defeat.

To Troy:  I am not sure slavery being the primary cause (if you are saying this) is reductionist.  If you read the secessionist articles I linked originally, it is clear that slavery was a central reason for secession.  And even if you believe in the States’ Rights argument, the question remains:  states rights in defense of what? People like Calhoun, Dew, and many others in Virginia and Kentucky–where the final emancipation debates were held before the war–make it clear that states rights was tied particularly, but not exclusively, to slavery and the protection of the peculiar institution.  In these instances, the clarion call to secession and war is clear and almost without exception noted by those who wanted to keep their ownership in human beings.

But the question why the North fought is a valid one.  Is the notion of Founding important here?  Was the Founding the only one at the time (nay, in history) created not be at open or secret war with the rights of mankind?  This question answered in the affirmative does not negate the dedication to the idea of human equality (rightly understood) when  considering the practical problems confronted with a freed race. If the Declaration is false, then there is no reason to emancipate; but if the Declaration is true, then emancipation becomes a moral and political necessity. 

The question is if Jefferson was right in his Notes and other private correspondence?  Even he as a slaveowner understood its corrupting influences; even he understood–along with most all other Founders (Madison, Washington, Monroe, Adams, with JQA, etc)–that is was an “evil” and contrary to the “Founding”.  The North, through Lincoln’s statesmanship (but even through those “sons of the Fathers who came before him), was dedicated to the Ancient Faith of the Declaration and the Constitution which is informed by it.  The South went as Jefferson feared it would go, and was perhaps corrupted by the institution which was a private teacher of despotism (as Jefferson noted in Query 18). 

You are correct that some things were hammered out later.  But as to the meaning of the Founding, the Founders were pretty much unanimous.  In this way, the Founders were pretty much Lockean, and Aristotelian; they rejected the politics of Hobbes and Machiavelli without exception.  If slavery is a good, and not wrong (and clearly the South generally changed on this between 1776 and 1850–from necessary evil to positive good), then nothing is wrong.  

There is no evidence, public or private, that the Founders believed the Founding was an affirmation of the natural human inferiority of one race.  The Confederacy was founded in explicit opposition to that idea.