I think I figure it out. Rebuilding the fleet style has worked. I was able to assign the same exact ship design to every fleet slot except one, the ship design did not show up, I believe because it wasn't the right size, so I used something close and saved the fleet style and it worked. I've already forgotten exactly which fleet slot it was, but looks like I'm going to have to go through each manually, which I am going to do.
I had to remove two abilities from the faction as well as change the ship color template, set the starting ship to survey ship, and change the star system to the random one for minor races. Aquilaran Hegemony is the only one I've completed. I'm trying to keep the traits that most match your civ descriptions.
I'm happy to provide the files back to you if you're interested in distributing a no mod required version.
EDIT: Just did the Arachnid Empire and it also worked so looks like this is a good solution.