Obviously Crusades brought many changes to game files making many mods not compatible.
Even my custom faction (xml not game generated) is not compatible anymore.
I'm terribly disappointed I hated specializations then I found TechTree editor which I could remove them. But now nothing works I have spent more time modding and testing rather playing.
I'm afraid I won't be able to play GC3 ever again, I'm tired trying...
If you want the game as is, fine but if you want it modded it's too much work.