In paranormal literature, an imprint is usually part of an energy field--left by a spirit, for example. Auras also can show whether you're happy, or fearful, that sort of thing, by whether they are expansive or hug the body. If he's supposed to be the reincarnation of Jesus, then I suggest that you use the analogy of remembering a dream or recalling repressed memories (controversial because of the blend of fantasy and suggestion, but they might make a good model). Also, maybe if you hear yourself when you talk to yourself, that could be useful. One person I knew heard a voice in his head that told him he couldn't be successful. Using an energy psychology technique, he "tuned" the voice up until he recognized it--it was his mother. So think of the times like that, when you hear a voice in your head telling you something--and maybe have Connor hear a voice, unbidden, like an ego-alien, say the Sermon on the Mound. He tunes it up (have him go to a psychologist or hypnotherapist, and as he hears the voice more clearly, he realizes it's his voice. Or better still, have him hear the voice of Jesus (from Zeferelli or others who have produced films), but as he tunes it up, it's his voice.
SPOILER ALERT. IF YOU HAVEN'T SEEN THE FIRST SEASON OF WESTWOLRD, DON'T READ FURTHER. Another possible model. Delores kept on having 'memories,'in scenes where she and Bernard were talking, and he was probing the breakdown in her programming. But when she finally gets to the center of the maze, she first sees Bernard, but she turns around and it's her talking to herself. Freedom and sentience is when you hear the voice of the gods as your own voice. SPOILER ALERT.
So Connor, in his way to self-discovery, when he talks to himself, at some point is talking to Jesus--and Jesus becomes him...Just thoughts and I hope I didn't spoil that part of WW to you if you haven't seen it.