This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
The narrator from "The Watchmaker's Apprentice" is the son of the doctor from "The Doctor's Wife"
Seems to be jossed. Both (or individuals that look very similar, anyway) have made an appearance in the comic, and look roughly the same age. There's also no indication that the doctor has a wife at this stage of the story.