I got the good ending, so she’s my wife and her body is in the portal room, but I’m still confused
So if she's your wife that means she must be in truck instead of Luna. If so, you should go back to empty room, and there will be soul orb. By obtaining it, you deactivate Faith as your wife, and after that you can see how she seats in truck lifeless. So now you just should leave university and go back home, where will be neither Faith no Luna. And now you go to asylum or sunflower city for your next wife. After that, soul orb can be found in place, where you found your current wife's body