You may already be aware of this, but on the FamilySearch site [Mormon] I found that a woman named Joan has an amazing genealogy on the Waite family which goes back to 1588 in England. She has a Francis Waite [bn SC] who married a Nancy Armstrong on 6/20/1837 in Wilcox Co., AL. However, she has ca 1795 as his year of birth. She shows him as being born in Abbeville Co., SC. You didn't mention the name of Francis' wife. Was it Nancy? Is it possible that the couple married in Wilcox Co. is the couple you are researching?
As I mentioned, the genealogy goes back quite a few generations in SC and in England.
Also, Francis' father is shown as John. Remember that there is a John Waite on the 1820 SC census.