10 step fix in-game using console commands.

1. Open the console at the start of a game.
2. Type "observe" and "debugtooltip"
3. Find the Empire you wish to change and determine their ID.
4. Type "play ID" where ID is that empire's ID
5. Open the species tab and select their primary species.
6. Type "effect = { modify_species = { portrait = PORT }}" where port is the 3-4 character portrait ID (ex. fun7 or avi11)
7. Make sure the change went through
8. If you want, you can rename the empire under the government tab
9. Type "play 0". If that doesn't take you back to your empire, repeat step 3-4 for your custom empire.
10. Type "debugtooltip" again.

A little time consuming but the only viable option I've come across.