Have you tried the denominations themselves? I hope that the PC(USA) could tell you how many members there were at different times. Now, denominations change & the Civil War did split many denominations. Some info here:http://history.pcusa.org/
The archives of a denomination's colleges or seminaries -- Macalester College is in your neighborhood -- could point you in the right direction. Central Methodist University in Fayette, Missouri has great archives of Methodists in the Midwest.
My ancestors in Iowa were Quakers, farming & tavern keeping. Named their youngest son Frederick Douglas Weaver....
Ethnicity & faith are related. More Irish & Italian immigrants were Catholic, more Germans & Scandinavians were Lutheran. Looking at waves of immigration might help.
Best wishes in your search!