Hi Byron, I am glad you have dived into researching the spouses of Jonathan, Whitcomb, Jr; I will eagerly follow your progress. I am afraid that have no evidence to offer, but I am interested because there is a pretty good chance that I am descended from Jonathan Jr and Deborah Scripture. That connection is not yet certain, because I have not conclusively connected my line to Ephraim, b. 1774, son of Reuben, b. 1747, son of Benjamin, b. 1711, who seems to be the only child of Jonathan and Deborah.
A number of genealogical sources lay the claim that Benjamin had a sister named Lydia. I feel the evidence is pretty strongly against that claim; the hypothesis that I like is that Lydia, if she really is a child of Jonathan, was born in about 1706 to Jonathan's previous spouse. If in your researches you establish where Lydia belongs, I would be glad to hear the result. I will stay tuned for any new developments in your research on this Whitcomb branch.