At present, my current preferred read of the sequence of events is:
Zagreus- The Doctor and Charley depart our universe for the Divergent Universe
Gallifrey I- "The Doctor is gone now"
Scherzo through
The Twilight KingdomGallifrey II through
Gallifrey IV- Choosing to break the DU story here is largely thematic, in that it performs the dual role of making it seem that Eight/Charley spend a very long time over there, while at the same time letting the Gallifrey civil war story play out uninterrupted
Faith Stealer through
The Next Life- The remainder of the DU arc plays out; when they return, they do so unfettered because R/L/N are gone to other universes and Gallifrey is in disarray
Terror Firma through
The Girl Who Never Was- Wrapping up Eight's story with C'rizz and Charley before taking a natural thematic break to turn back to:
Gallifrey V and
Gallifrey VI- Returning to R/L/N's stories after they've been away on the alternative Gallifrey for at least a year; they return to our universe, reset Gallifrey, and unintentionally apparently launch the Time War
Gallifrey: Intervention Earth- Though actually set much later, it needs to be listened to at this point for Enemy Lines to make sense
Gallifrey: Enemy Lines- The future seen in Intervention Earth is erased, Omega remains trapped in his pocket universe, Romana's Presidency comes to an end and she takes over command of the CIA with Narvin her continued ally
Eighth Doctor Adventures entire run
- The CIA, headed by Romana, thinks to/is able to place Lucie Miller with the Doctor. They have their adventures together, until the fruits of Gallifrey VI result in the Dalek Time Controller/Lucie Miller story that ends the EDA run. (Admittedly, assuming that the reason for the CIA selecting the Doctor is due to Romana is a bit of a fanjodrell)
Dark Eyes 1- By this point it appears that, in the background, the regime on Gallifrey has changed completely. There's a male President, and Straxus is Coordinator of the CIA, and their plan together is to try to retroactively erase the Daleks from history, which (to me) slots in very nicely with the building conflict between the Time Lords and the Daleks
Dark Eyes 2-4- Further proof of the regime change: Narvin has to manipulate the past in order to install himself as Coordinator-in-Extremis of the CIA to assist with the Eminence/Dalek Time Controller crisis
Doom Coalition- Another President is referenced (though it's not clear if it's the same one from DE1 or not). Explicit mention is made of "a past regime" having opened up the Academy to alien races, a direct reference to Romana's reforms in the first couple series of Gallifrey
I will emphasise here that this is my
current read of the sequence of events. I often change my mind, finding the new explanation to be better than the old. But because this has happened before, I may well change my mind again