I assume by "put the mod" you mean take the 7zip file, move it into that Modding folder, right-click on it, click "Extract Here"? Also, that Modding folder doesn't exist, so I made one named exactly that.
You may find this somewhere on the mod thread of Amplitude/Endless Space forums. Unfortunately it has been such a long time since I made this that I genuinely wouldn't be able to give you a very useful answer.
Look at what weapons you've put on your ships, and try something different is what I would recommend. There's some clear rock-paper-scissor mechanics and all weapon types are important.
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Quick Guide
1. Put the mod here:
C:\Users\<name>\Documents\Endless Space\Disharmony\Modding
2. Go to your Steam library, right click the game, select "properties". Under "set launch options" put in
+mod ImperiumAeternaAlso, that Modding folder doesn't exist, so I made one named exactly that.
EDIT: Yes, this works.
Look at what weapons you've put on your ships, and try something different is what I would recommend. There's some clear rock-paper-scissor mechanics and all weapon types are important.