I'd go with (for initial testing purposes):
Government - Theocracy already stops non-state religion spread, increase state religion spread. Don't see why any of the others should have an effect. Reduced (?%) missionary cost.
Religious -
Folklore: Slow all religions spread
Divine Right: Slightly increase state religion spread
State church: Increase state religion spread, decrease non-state religion spread. Somewhat reduced (?%) missionary cost.
Religious tolerance: Increase all religions spread. Somewhat increase (?%) missionary spread.
Intolerant: Already stops non-state religion spread, greatly increase state religion spread. Reduced (?%) missionary cost.
Freedom of religion: Greatly increase all religion spread. Increase (?%) missionary cost.
Abolishment of religion: already stops all religion spread. No prophet specialists/GPs, no missionaries allowed.
Immigration -
None: No effect.
Open borders: Increase non-state religion spread.
Closed borders: Decrease non-state religion spread.
Skilled labor only: Slightly decrease non-state religion spread.
Secure borders: Slightly increase non-state religion spread.
Education -
Religious Training: Increase state religion spread. Slightly reduce (?%) missionary cost.
Mind control: No religion spread, -90% missionary cost. (you control their minds... they believe what you tell them to!)
Commerce: Just a basic more trade = more non-state spread, less trade = less spread. Barter would have no effect. The 3 missing civics would all probably have an effect as well.
May have missed some, just wrote this between turns in my current game. I'd drastically increase the hammer cost on missionaries if you implemented all this, so religions would spread more naturally, based on your choices. You COULD still spread them manually... but it would be costly, while running an extremely religious setup would make missionaries spammable. Don't know how feasible all this is, or even if it should be implemented (how would the AI handle it?), just something I thought of all of a sudden while looking at your civic remake.
What are your thoughts? Good? Bad? Totally IMBA? Can't believe you wasted your time reading this post?