Txurce
Deity
From this, I think Monastery or Monastic School works well (though Txurce and pthmix are right, a flat bonus would be more fitting), Universities seem to be at an appropriate place and science on villages should unlock at Printing Press. This last is far more historically accurate and would prevent messing too much with the early-game science balance. It would make for an interesting transition in the mid-game away from pop-based science to terrain-based science, giving incentive to expansion and land-grabs which seems historically accurate in my mind as well for the time period.
A high-tier building would be much better if you're willing to code it (great to hear it's feasible!) - the only reason I suggested a policy is because I was under the impression you couldn't create such a building.
Your "Printing Press" trigger is basically my earlier Renaissance trigger - so of course, I agree. I also think we need more than one additional building (a la Sukritact) or it's too easy for a wide empire to emulate this approach. As I mentioned earlier, multiple buildings work in that you can only build so many of them. (Anyone would just knock off a monastery.)
This also allows population to have more of an effect for longer, as I believe it should. I'm happy to support Thal's desire to change the system, but there's nothing passive about building a large population: it requires multiple buildings, and increased happiness demands. In many ways, shifting it to villages is actually more passive (build it and you're done).
The gold issue you raised earlier is something we should not lose track of. As it is, we are still dealing with the blowback from having the AI spend all its gold. In my last game America had countless frigates, and partly as a result of the crazy unit building, for the second game in a row almost all the AI were hopelessly broke in the later game. Adding more gold may alleviate this problem... or it may make it worse.