My guess is it would mostly be a clash between Protestant and Catholic or Christian and native religions.
Did Protestants ever try to stomp out Catholics. Vice versa?
Follow up: Were Catholics upset about the massive influx of Protestants?
Where there are not many religious conflicts at all?
I just thought I would ask in case somebody knows, thank you!
The biggest one you seem to leave out would be the Mormons. The US even essentially declared war and sent troops to Utah when they thought they were trying to break away!