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Anyone want to share what they think the best configuration of cities with universities and bishoprics is for maximizing tech rate without wasting too much on the "too far ahead" penalty?

Universities are better than monastic schools, obviously, and they also cost more. I don't see how you can avoid the 'too far ahead' penalty...if you've got enough schools and universities built, then you'll eventually get ahead of your time, that happens. You should keep in mind that cities make a lot more cash as well, while bishoprics can end up not paying you at all.
 
If your capital is coastal (like London), then it's worth building a second city regardless.

Not sure whether multiple universities in the same province will stack their bonus or not.
 
I guess building the research buildings in a church is "better" because they cost far less put together then the 1 city research building you can build within a resonable timeframe. 320 for the 2 church building compared to 600 for the first city building. I think you need lvl 3 city infrastructure for the second city reserach building maybe even lvl 4, i forget.
 
If your capital is coastal (like London), then it's worth building a second city regardless.

Not sure whether multiple universities in the same province will stack their bonus or not.

If you're gonna choose between a bishopric and a city, obviously go with the city, it makes you a lot more money anyways. Personally, I never build bishoprics, I either go with castles for quality troops, or with cities for cash; I also make sure my demesne holdings are always coastal. The whole university thing is just a plus. I also assume that these bonuses stack, it would be silly if they didn't.
 
If you're gonna choose between a bishopric and a city, obviously go with the city, it makes you a lot more money anyways. Personally, I never build bishoprics, I either go with castles for quality troops, or with cities for cash; I also make sure my demesne holdings are always coastal. The whole university thing is just a plus. I also assume that these bonuses stack, it would be silly if they didn't.

Usually the building of churches is reserved for the under-developed provinces that don't have one yet, like most of the southern Baltic pagan provinces.