The Jihad is most likely, the 40k refugees really latched on to ComStar and the Word of Blake, I think. To get a video game.
If I was going to do a video game I think the Chaos March is where I'd do it. So that could be Civil War or a significant chunk of the Jihad.
The HPGs ceasing to work, in general, because of something the Wobbies/something left over from ComStar causing a Dark Age is fine. But that should result in a large amount of civil uprisings. Civil War o'clock for the entire Inner Sphere, not just Marik. Everyone, even the Clans who were using old ComStar infrastructure.
And then the Dark Age should be focused on rebuilding HPG infrastructure and re-conquering and re-structuring the various Great Houses, and Clans. This is also the time that several abjured Clan empires form after the Wars of Reaving and the Society trying to become top caste. As the Dark Age resolves, these Empires/Khantes should start trading/skirmishing with Inner Sphere factions. I'd love it if one or two of these factions took the very long route to the far side to interact with whatever comes out of Canopus or the Concordat.
The Republic of the Sphere? Maybe salvageable? But not the way they did it. A new Terran empire forging itself out of the worlds all broken away because of the Dark Age is very plausible. Large chunks of everything else is fucking dumb. And certainly everyone disarming or 'disarming' needs to go away.
You actively have several groups in the Inner Sphere still hellbent on conquering everything, along with pirates. Disarming is fucking dumb.
The Fortress time with the somehow interdiction of JumpDrives? That should probably go away too.
But it being held together by strong Devlin Stone and collapsing as Clan Wolf invades to become the ilClan (though nobody should give a fuck) just as Devlin Stone starts slipping (due to advanced age), I think is the tweak I'd make.
Things I'd like to see happen in the ilClan era: Find Centrellas who are pissed at the Liao's basically usurping the Magistracy, another Arano restoration (The Cormorant Rises Like a Phoenix!) because I actually like that faction and that section of space could use a wedge, several new Periphery states to form and actually stick around for a while and be meaningful on the outskirts of old Lyran and Drac territory, and I want to see the FedSuns make serious (but not too serious) gains.
Also, I think a smooth-ish re-establishment of the FWL should happen so the Purple Eagle can actually be relevant for an Era instead of dealing with Civil War O'clock.