Intuitively I'd say:
"I just saw the Doctor regenerate in the Christmas special. I love how her first words were "Oh brilliant", although I had to rewatch it five times until I got what she was saying."
"Back when she was still in her first incarnation she was quite enigmatic."
"I just rewatched the Sixth Doctor's era and he was a real asshole."
So, male pronouns if referring to a specific previous male incarnation, female pronouns if referring to a specific female incarnation or the Doctor in general. I guess.
"I just saw the Doctor regenerate in the Christmas special. I love how her first words were "Oh brilliant", although I had to rewatch it five times until I got what she was saying."
"Back when she was still in her first incarnation she was quite enigmatic."
"I just rewatched the Sixth Doctor's era and he was a real asshole."
So, male pronouns if referring to a specific previous male incarnation, female pronouns if referring to a specific female incarnation or the Doctor in general. I guess.