I've noticed a few things to fix.
One of the things that stands out in your game is that you have 8 colonized nebulae, each with The Great Link, for a whooping +8 morale empire-wide; I guess that's a bit of an overkill
I should probably revert it back to OnePerEmpire The idea was not to make it that strong...
The K-W Factory and the Vorta Cloning Lab should enough of an advantage. Even the Cloning Lab might be a bit much.
The Klingons declared war on you this time You have no allies and are involved in a few wars, so chance was much higher. Might have something to do with them being working on an affiliation with the Romulans.
One thing I'm not sure about, should all those member minor races be declaring war on the Klingons Or should only allied empires do that?
(their status didn't change though, so that's something to look into)
Member minor race colonies are ok, need to test subjugated minor and faction colonies.Still needs to be tested in member and subjugated colonies though.