James Madison, Memorial and Remonstrance against Religious Assessments, 20 June 1785
http://press-pubs.uchicago.edu/founders/documents/amendI_religions43.html
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Strongly guarded as is the separation between Religion & Govt in the Constitution of the United States, the danger of encroachment by Ecclesiastical Bodies may be illustrated by precedents already furnished in their short history.
James Madison, Detached Memoranda ca. 1817
--http://press-pubs.uchicago.edu/founders/documents/amendI_religions64.html
When speaking of the fundamental values underlying religion of his day, where those religions were not state religions but operated by the people themselves, IMHO Mdison was just as clear on his advocacy.