Evil isn't set after those stories. It's just dawned on me that I've used "Civil War" to refer to two different conflicts, so sorry if that caused any confusion. To clarify:
- The Dalek Civil War is the one between the Humanised Daleks and the Emperor that happens in Evil. This one stems from the Great War which links it to Master Plan, according to the Evil novelisation.
- The Imperial-Renegade Dalek Civil War is the one against Davros and the Emperor. This one has roots in the Movellan War and spans from Resurrection, Revelation, Emperor!, Remembrance and War.
The Dalek Civil War happens first. Peel's Evil novelisation treats it as a kind of finale to early Dalek history. His novelisations were mostly interconnected while also tending to incorporate elements or aspects from The Dalek Chronicles and the 60s Dalek annuals. This is the period of Dalek War Machines and Silver Daleks, the Golden Emperor, the "irreplaceable" Black Dalek Leader and unstable taranium time machines. It this Civil War that Lights, Bringer and Children are talking about. This early era appears to look roughly like this.
- Genesis (either one), The Daleks/Chronicles, Invasion of Earth, Dalek Book, Dalek World, The Chase, Outer Space Book, Master Plan and Evil
After that comes Day. It's never explicitly said to come after Evil but the Daleks have better time travel by then, they know the First and Second Doctors, and in the Day novelisation, the Doctor says "I thought I’d destroyed them once before, but I was wrong." Conquests suggest this is the point at which the Time Lords start taking the Daleks seriously.
Eventually they get to Frontier and so on, and follow the rough timeline laid out in the previous post. The Daleks exterminate their merry way through time and the universe until Davros comes back during the Movellan War and starts challenging the Emperor/Prime's authority. And that's when the Imperial-Renegade Civil War happens.
Therefore, minus one (apparent, but unseen) death aboard the Death Wheel in Nemesis, the Prime could have a clear run from Genesis all the way up to Emperor!. Then it's just a bridge between Emperor! and War.