Is he moving around doing things in the dark, that could be freaking her out? My H gets ready in the AM in the dark if I'm still asleep. Maybe she just needs to be kept away from him in the morning while getting ready.
Do you let her know that acting like that isn't OK? Ignoring growling aggressive behavior isn't the way to deal with it. She will think its acceptable to keep doing.
I'd consider talking to or setting up an appt with a behaviorist if it continues.
Where is she when she is barking and growling? On her bed, on yours? Could it be a territorial thing?
Does she bark at him any other time of the day? In any other location?
How does he play with her, rough or gentle? Is it more with him putting his hands on her or playing tug with toys?
Like the PP said, if it is in a dark/dim room, she may not see him the best and is reacting to that versus any type of true aggression.
These are the questions I was going to ask. Does she sleep in bed with you? Where is she when she's barking at him? If she sleeps with you, who gets into bed first?
I'm sorry your dog bit your BF. I think speaking to a behaviorist is a good option, but that route could be costly.
When BF gets up to shower, at that time could you leash or tether her to your area so BF and her are separated? There is that fine line of respecting each other boundaries. Maybe she feels threatened by the water or him moving around (if he's in the dark)? Did your ex beat her when it was dark or spray her with water for punishment? Maybe she associates the two?