I use a slightly modified 1248, 4th Imperial setting.
Big differences IMTU are:
Unbeknownst to everyone other than the Cyms and the Viral packs, the modifications to the Cym chips that resulted in the Virus did not last past the 2nd generation. 99.9% of "Virus" IMTU are actually Cym chips as per Signal GK. Viral insanity comes from Cym series groups with no dominant Cym chip. While this slows the spread, as a chip now has to physically enter a system to take it over, it in no way makes them any less deadly or versatile. But it does allow for Cym PCs, and limits them to one "body" at a time.
The Empress wave is only a Psionic component, the Hard Radiation component having effectively died some 30k parsecs towards the core. One additional effect that is unknown to most of charted space is that any world that once held a Chirper Population, gains a Droyne population after the wave front passes through the system.
The 4th Imperium has just made an amazing breakthrough in drive systems, and a very small number of Hop 1 prototype drives have been made available to Emperor Averys hand picked agents to test and use in the course of their duties. The existence of the Hop drive prototypes is a very closely guarded secret known only to a very small handful of people in the 4th Imperium.
Finally, Grandfather lied. The war isn't over yet. There are still a few other Ancients out there...