Welcome to the Org, Kolvorok!
Unfortunately, some things about the game are hardcoded. The happiness effect of the faction leader across the empire is one, as is the conversion rate to the faction's religion. gollum is on the money with the building conversion rates though, they give both a happiness bonus and a high conversion rate, which knocks back the chance of rebellion quickly. Another point, the religious buildings are in separate building lines, so the bonuses for happiness and conversion stack. A Church and a Monastery will give a combined total of +30% to happiness, and 20% conversion. The standard Bishop is only 2% conversion.
You are correct in how to change the province unrest factor in the startpos file. The building conversion is set in the build_prod file, column 22 (Faith Propagation). The conversion for agents is in the unit_prod file, column 67 (Faith). I think any unit can be set to add conversion, for grins you could make Ghazis or Fanatics convert a small amount. I've always thought that Ports/Merchants might be a good place to throw in a small conversion rate for all religions (even Jews/Heretics/Pagans), more contact with the outside world would encourage religious experimentation and immigration, and might liven things up a bit.
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