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There is more on Jacob F. M. Rockefeller and some of his descendants in "The Transactions of the Rockefeller Family Association," ed. by Henry Oscar Rockefeller, 1910, available online by subscription at Ancestry.com.
Jacob d. in Salt Lake City, UT in 1882. A son, James, died in California in 1861, obviously he did not stay in Stafford County, VA with his mother and sisters where he appears in the 1860 census.
I can't find Jacob in any census. Working for the railroad, a growth industry at the time, is still a plausible explanation. The Rockefeller book has no mention of any remarriage.