Or, were there any early theological battles tied to politics during the period after the civil war? Basically, I want to try to understand how, in a concrete sense, Southern Baptism was branded a republican institution. Did this happen 'intentionally', or was it an organic process?
The alignment of Southern evangelicals with the Republican party is much, much later than I think you realize. You don't need a 19th century historian; you need a mid-20th century historian. Prior to that, Southern evangelicals generally went firmly Democratic. I'm not qualified to explain in detail why, but I would look up the Southern Strategy and the general political realignment of the South as a result of the Civil Rights Act.