In response to #2 -- It's important to understand historical events in their context, and not judge them from our own perspective. Jefferson meant "all men are created equal," period. Where those different men landed in their society was not the Creator's issue; what Jefferson meant was that we are created out of the same dust with the same Natural Rights, peasant or king. What each man did after his creation was up to each man. Jefferson is putting the final nail in the coffin of the concept of the "Divine Right of Kings," which plagued humanity for millennia, and caused the British Colonies in America endless trouble. His phrasing was meant to say that all men have the same rights (not the same abilities!) , and are responsible for their own governance, and that the era of governance by a king in the colonies is over, since they each have their own legislative assemblies. To state this in a world which had no democracies since Grecian times was indeed revolutionary. What we may see today as "minority rights" was certainly not a consideration for the Founders. Two and a half centuries ago male Africans were not considered men; women of every race around the world were consigned to the domestic sphere, because a woman's sole job in that time was to birth the next generation, and that's all women could do, so many dying in childbirth. The argument today that the Founders did not go far enough is irrelevant, and disrespectful for the struggles they had to endure to even go as far as they did. What they did in their own time was fantastic enough. They got the process in motion, and individuals since from later generations have furthered the cause of democracy and freedom for all members of humanity, to a degree the Founders would marvel at. How far we've come in a couple hundred years!
in 1619, Virginia established the House of Burgesses as the first example of a legislative form of government to counter the governor and his council, and to answer to Parliament in London. This expanded the notion that colonists could have political influence; although not a direct democracy, the principles of democracy and freedom established in the Virginian colony helped establish the political arguments the American Colonies had against Britain century and a half later. That same year, 1200 colonists arrived in Virginia, including the first handful of Africans as slaves, although at this time there were Black colonists who owned their own land, could vote, and owned their own slaves. The conflicting institutions of slavery and freedom, established in 1619, created a paradox that determined the course of history for Virginia and the United States for centuries.
One of the most glaring examples of a contradiction would be the hypocritical nature of the Puritans who settled the Massachusetts Bay colony. From a young age, American students are taught that they came here from England to find religious freedom and escape persecution for their beliefs. They were hated and persecuted in England, it is true; they were considered extremists and their notion to "purify" the church of all remaining Catholic influence earned them more than a few enemies. However much they sought freedom, however, their Massachusetts colony was a bastion of intolerance and fear--fear of God, fear of Satan, fear of going to hell, fear of witchcraft, fear of anyone challenging the established ideals. Roger Williams and Anne Hutchinson are probably the most well-known, but certainly not the only Puritan dissidents. About 150 years later, another one of America's more interesting contradictions occurred when Thomas Jefferson, a slaveowner, penned the words "We hold these truths to be self-evident that all men are created equal." Although historians acknowledge that none of the Founding Fathers would have construed that phrase to include all Americans at the time it was written, the glaring inconsistency cannot be ignored. A more accurate, but less poetic line might have been, "We hold these truths to be self-evident that all educated, fairly affluent white men are created equal." In the years since, laws and amendments have extended America's promise of equality to blacks, women, the disabled, etc, but these rights were dearly won, and many would say that our nation still yet doesn't truly believe that we are all created equal.
The early American experience, as well as, the early United States experience holds more than a few 'contradictions'. The obvious ones encompass free religious practices and equality, namely the practices of the Puritans and the immortal lines of Jefferson. However, there were many others, among them the 'witch hysteria' in New England, the 'so-called' free press (research the Zenger Case) and restrictions upon natural rights (The Alien and Sedition Acts of 1798)
I think the importance of your question lies not in the contradictions (of which there were many ) but in the quest to reconcile ideology and reality. Ideology is the way we would like experience to be, reality is the actual experience. That is the core of those 'contradictions' you ask about. Ideology and reality rarely intersect at the designated point, which is why these 'contradictions' have existed, and still exist, perhaps there will always be a disconnection in one form or another. We are the first nation born out of the aspiration that ideas have the potential of becoming reality. This in and of itself is a contradiction, and as a result the self inflicted wounds of the United States have been her most damaging. However, if our goal is to aspire to... We The People....it just might be that our 'contradictions' (as bad as they might have been) remind us of the definition of aspiration, and the importance of that ideal to our 'American Sense of Reality'.