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In my research, I have found that family stories are not always accurate.
Carlisle Indian School was not founded until 1879. Perry would have been 30.
Although the Orphan Trains started in 1854, they took street children from the slums of New York City west. Many children were adopted, although many also ended up as cheap farm labor. While the trains were running when Perry went from Kentucky to Missouri, it is not likely he was on one. Given his father's death in 1858 in Trimble County, it is much more likely he went to live with his sister, Eliza, (who was still in Trimble County, KY) and then moved west to Missouri with Eliza and her family around 1858 or 1859. The 1860 census in Missouri shows Perry living with Eliza, and her husband, John Kelly. By 1870, he had his own farm.