I was sort of playtesting it, so I played on chieftan level (that way I would make sure to be able to build all wonders ahead of the other civs). I was very puzzled with the sewer system thing myself... and yes, I had built Jellingstenen as well, quite strange that the churches gained from that wonder don't count as churches for the other wonders. Maybe those bugs wouldn't be there if it was a Conquests scenario ??
As for Kronborg and Round church, I had invaded Bornholm, so I was the sole owner of rock

In the beginning I could build the Round church, but I wanted to build one of the extra capital buildings on Bornholm, just for the fun of it, and then, suddently, I couldn't build the Round church

I accidentally destroyed my save game

I was just around 1290 or 1300, at the beginning of the modern era, having conquered all of Sjælland, Bornholm, Skåne and 2 cities from having all of Halland... I spent much more time improving than conquering
Anyway, I enjoy the mod alot, and hope you'll make a Conquests version of it
