At the point where it's 85% or higher, I leave a cardinal in place to continue the good works, and move the rest of the holy wrecking crew on to new, less tolerant hallows of evildoers (like that nest of heretics in Finland). I don't need 100% conversion, just something close to it.

I don't recall how the level of faith and the level of fanaticism affect happiness in general; can someone more knowledgable than I supply a brief synopsis?