What were some challenges for Thomas Jefferson while he was writing the Declaration of Independence?

Jefferson had to deal both with the contradictions within his own life and thought, as well as with the possible objections by much of Congress either to his saying too much on "sensitive" topics or not saying enough.
As is well known, his initial draft included a paragraph criticizing the King for allowing the slave trade to continue. This, as Jefferson later indicated, was not acceptable to those members of Congress who themselves held enslaved people. But Jefferson himself, of course, was a practitioner of slavery. My guess is that he must have realized, at least on a subconscious level, that it was hypocritical for him to blame the King for the continuance of either the slave trade or the institution of slavery itself. The only allusion to slavery in the final version of the Declaration is a euphemistic one, saying of the King that "he has incited domestic insurrections among us." This refers to the sporadic recruiting by the British of enslaved people as troops with the promise of freedom to them. One also must ask if Jefferson might have struggled inwardly over the clause concerning the indigenous Americans in which they are described as "merciless savages." Jefferson was an admirer in general of the spirit and character of Native Americans, as he expressed in other writings.
A second major issue, though this has received less attention by commentators over the years, involves religion. Jefferson and many others in Congress were deists, rejecting not only organized religion but also, for the most part, the belief that God actively influences human affairs. Interestingly, however, Jefferson's original version stated, "We hold these truths to be sacred and inviolable: that all men are created equal." Most scholars believe that when Franklin and Adams made their preliminary review of the draft, it was Franklin who amended "sacred and inviolable" to "self-evident." Though there is not necessarily anything "spiritual" or based on religious belief in the use of the word "sacred" in this context, Franklin's word choice is more purely secular and "human." It is also more eloquent.
It was when Congress as a whole reviewed the draft that more extensive changes were made. Jefferson had already written that men "are endowed by their Creator with certain inalienable rights," but Congress made additional references to God which, in my opinion, actually improved the document. The phrases "appealing to the Supreme Judge of the world for the rectitude of our intentions" and "with a firm reliance on Divine Providence" lend a gravity to passages which in Jefferson's original seem more lightweight and dry.