Originally posted by The Wizard of Oz
Essentially, is the transition from pre-Contagion to post-Contagion just a particularly bad spot in a decline that was already happening (like the fall of Rome) or a total destruction of what, while it may not have been at its height, was still a mighty civilisation (like how people imagine the fall of Rome).
Somewhere in between. The Shogunate was wracked by internal warring to a very real extent, but the Contagion resulted in mass destruction of infrastructure beyond what had come before, paired with a massive loss of institutional memory from those who died of the plague and its aftermath.
The "Records of the Before" chapters in the 1e Aspect books remain the best available resource for the Shogunate.