>You still having issues? You have all the Expansions?
Thanks for asking.
Yes, I have all the DLCs Steam has to offer except the races of Star Control.
There still are some issues.
As I mentioned before, Handy and Klutzy traits are swapped, I had to manually edit RaceTraitDefs file to restore negative and positive values the way they are in vanilla file. I believe this has got something to do with it:

Other of the mentioned issues.
Here is my savegame https://drive.google.com/open?id=1XlPILHGdnnz1vQew8_0G_eULbzVDrwPk
If you desire you can load it and see what would happen. At this savegame I'm seeing bugged mercenaries (picture below), and my research governor stopped working after constructing a couple of buildings (this may be vanilla issue though).

The issue with mercenaries disappear if I remove the EXP1_Mercenary module.
I do hope I installed everything correctly. This is what my CG3Crusade\Mods folder looks like:

And one more thing. Which one of your statements is correct:
"Delete the Core, GC3 and Partiles.bin files from that Mods folder, they are suspiciously large."
or
"Which it should (It is the game Cache)."
I mean, some things are obvious for folks who have been playing and modding GC3 for years, but not for me. I've just spent a week with it 
Thanks for the mod and for your effort!