Concerning Sally and the desolation of Mobius, it seems to me you set up the Genesis Wave to be responsible for that. After all, when Eggman announced it on the last page of Issue 1, Mecha-Sally was there too, which implies she has a direct connection to it in some way. The only other canon thing we know about what happened before Doomsday is that Naugus got his hands on two more Emeralds, but that isn't necessarily important in the present.
What I noticed on my recent run-through of the comic is that, unlike most people who try to wrap up the series, you're not content to simply resolve matters, but you create new sources of conflict so that the tale naturally continues. Lara-le is still hiding someone in Albion, Remington's grief and anger are eating away at him, and undoubtedly you've still got plenty more twists up your sleeve.
My hope is that the next page will have some interesting flashes of what Silver sees, but then again you could make it all secretive and just show him freaking out about something.