The Endless Ghost turns out to be the [Watcher of the Gold]?, who is on his way to reuniting the [Gold Casket]? with the other polarities in Time City. Because the [Silver Casket]? and the [Iron Casket]? have fallen into the wrong hands, the [Lead Casket]? is used to prevent him from reaching his destination, and potentially delivering Time City into the control of the megalomaniac Lee family.
The Time Lady has been asleep beneath Time City the whole time, in the place that legend says is the resting place of Faber John. Faber John himself has been out watching over the polarities: each of the four guardians is an aspect of him.
Also in Time City the whole time has been the Lead Casket, which is the egg-shaped thing that the children have been using to travel through time. The reason travelling with it sometimes has erratic results is because it keeps being dragged off course by its attraction to the other polarities.
Dr. Wilander is the guardian of the Lead Casket [although I don't recall at this point whether he remembers this]. (It's not explicitly stated, but considering what "Faber John" means, his alias is surely a hat-tip to the Norse folk-hero Volundr, known in England as Wayland the Smith.)
When the four guardians reassemble themselves into Faber John, Dr. Wilander is the one he most obviously resembles, and he continues to occupy Dr. Wilander's rooms at [Seldom End]? (despite Sempitern Walker's assumption that he will want the Annuate Palace back).
Although Faber John and his wife will be living in Time City for a while, sooner or later the polarities will have to be redistributed so that Time City can carry on for another Platonic Year. It is suggested that this time Faber John will sleep through the centuries, as in the legends, and his wife will guard the polarities.