Played a couple of turns and get an CTD - Last entry of the debug.err file is "Debug Message: EndTurn 16"
I've seen that error before. In my case, at the beginning of Turn 17, a mission ship had to be launched. I had inadvertently deleted the mission ship in the fleet designer, so when the game couldn't find a missing resource, CTD.
Start with your last modded file and see if you're missing a resource, like a ship or building upgrade.
The game won't launch if there are significant XML errors, so you can rule out anything too blatant. Use your last saved game to recreate the problem. What happens during turn 16? Turning on the feature to show all notifications in the options menu might help too.