Sorry! Couple busy days at work, I'll try to get a long answer in the weekend, but the short version is that you need to go to your save directory, unzip the save, open it with a text editor (notepad++ for instance), search the names of the empires and species you want to change, and change their names, ethics, portraits ... Then save the file and recompress it.
EDIT: Actually, I'm working abroad for a few months, and don't actually have stellaris on my laptop or any saves. If you can send me one, I can point you to where the things to change are.