The more I think about it, the more I think Kas's plan makes no sense.
He wants revenge on Vecna. However, if he doesn't interfere, then the Wizard Three create a super Wish that unravels Vecna's ritual. Kas could then run up on him and kill him, or he could have approached the Wizard Three, lied to say he was reformed, and then told the truth about how the Rod can banish Vecna back to Oerth to be properly killed.
No matter how I try to cut it, replacing Mordenkainen is a Chaotic Stupid move. It sabotages his own plan for absolutely no real gain. So, how am I thinking about cutting it?
Evernight is the solution to my problems. The first piece of the Rod is here, in Evernight. The players return to Evernight after the FIrst Chapter; their dreams due ot being attached to Vecna allows them to process the secrets given to him, and one of those secrets is how to stop him. At the same time, the Silverhand is doing her thing. When the players get the first Piece of the Rod, the Wish STILL summons them. Kas is just flat out there, and the real Mordenkainen, and after some prep and discussing with each other what's going on, each of these four NPCs (Tasha, Morde, Silverhand, Kas) are able to discover ways to get to four more additional parts.
Once we get to the Miska part, where the 7th piece of the Rod will be located, Kas will betray the party and abscond to Pandemonium. The Crown of Lies masked his true intent and character, and it caused him to appear sincere and indeed STILL HUMAN to the party. When he acts on his true intentions, the Crown of Lies reveals him as the vampire that he truly is.
Now, that being said, something I want in the adventure in Vecna working against his foes. I don't want him to work against the PCs, but I do want him to work against the Wizard Three, who he should have some kind of history with. This would be in the form of putting a bounty on their heads for his cultists across the Multiverse. After all, why have that cool "battlemap" of the Sanctum and not have it get invaded by undead and demons?!
I think Lolth specifically knows about the players, especially after they ransack Web's Edge. However, she keeps that a secret, and the knowledge that Kas is working with the Wizard Three. This lets me have a brutally tragic climax where Vecna is ruined by Kas, admits the real reason for the ritual, and both are then struck down and send into Domains of Dread, leaving Lolth behind to harness the huge amount of power gathered by Vecna.
I think I'll take a page out of Out of the Abyss for the ending if I run it. The final battle has two parts. Part 1 is Lolth vs the players as other gods. I'd give them a sta tblock for Tiamat, the Raven Queen (wants the secrets Vecna gathered to figure out who she was), Elistraee, and Correllon. This fight weakens Lolth to CR 30, but also weakens the other gods, and allows the players to come in and finish the job. Lolth is defeated and retreats to the abyss, to scheme again another day.
Alternatively, the Rod of Seven Parts can be used to weaken Lolth, forcing her into a CR 30 form for the players to fight.
I think this line of events makes the adventure more runnable and also gives it a more coherent narrative throughout. It also has a lot of room for change, and of course the gods used can be subbed out for others as per taste, etc.
Anyway, that is how I'm feeling atm.