OK...Stephens didn't say in his quote that "man" didn't have god-given rights, he said the "NEGRO" did not. This was a common belief, even held by Lincoln. The Founding Fathers certainly were not refering to slaves as "equals", when they wrote the Declaration of Independence, as many owned slaves themselves! I am quite sure you must realize that!
No, Lincoln did not think that.
He states that he might not have felt the Negro his equal in many areas, but that the Negro had the same rights as any other man, and the Declaration was directed to all men.
This view of the Declaration, that it was meant only for white men, was a recent view, one pushed by Taney and Douglas.
No Founder of this nation ever suggested that the Declaration did not mean that all men were equal before God.
That slavery existed was a burden that the Founders sought to end (blaming the British King for it) by limiting slavery's growth.
If you want Lincoln's views on this, I would be happy to give you the page numbers from his writings.