Several months on and I've been slowly adding new civ/leader mods to my game, and I'm starting to get random CTDs similar to those I was experiencing before.
Only using YNAMP with closer cities, dover tweak and less barbarians, historical religions and several additional civs and leaders.
I wish we had some better way to diagnose crashes and mod conflicts rather than slowly adding mods 1 by 1 :/. Would be a huge help to modders trying to maximize compatibility.