I may be wrong with what I suggest here, but it is what I would do at any rate. Also note that I have no experience making a world where everything goes or a kitchen sink setting as you put it, and I’ve always had trouble playing or understanding such settings e.g Troika, so there’s all the disclaimers out of the way
What I will try to address is your Focus struggle that you highlight in the pitch as I believe the other two will be far easier once that is resolved.
I think you are right in that you need a Main Thing as you put it, but what leviathan oil does for Dishonored and what Precursor tech does for Numenera (I assume that is how Numenera works, I’ve only ever seen art of it) is it gives the settings a reason for their genres/tropes to work well together. A setting working well comes partly from consistency. Consistency comes partly from history. Perhaps defining some history for the world would be a start!
I think you have made some very correct steps so far in defining this setting. You have your inspirations laid out, you have some art that you feel is fitting, and you’ve defined some pillars of how you want the setting to technically work. Another thing you could do is write down themes you want the setting to be about.
What does Divinepunk mean? Do people rebel against Gods? If so, is one’s relationship with faith, the divine and supernatural a possible theme?
You mention witchcraft, ghouls, ancient AIs and shapeshifters. Great! Draw some mental lines between those. What is that relationship defined as? E.g. how are ghouls and ancient AIs related? What do they each think about each other and does one owe its existence to the other, or did one contribute to a significant change in the nature of the other? What themes might come out of that? If ghouls are how I know and understand them (undead) and you also have AI in there, a very good theme might be “what does it mean to be alive? Are AIs alive? Are ghouls?”
Once you have a list of such narrative (as opposed to mechanical or meta pillars) themes, you will have a list of the kind of stories that will most probably be told in the setting, or the ones you yourself want to tell. Those stories will have a specific tone and mood through those themes. That tone and mood is all that Dishonored and EB has that you are looking for, I think.
That’s the narrative part done. I don’t know if you would need a Main Thing in terms of something concrete in the world, like leviathan oil, a McGuffin like you say, but if you still feel that way, perhaps what I said about defining some history might help. The process can be largely the same as I described above about drawing lines between things. Try it with the Societies! What does the Ziggurat think of Red-Town and vice versa, and why? If you want you can center that or any other relationship around a McGuffin like a resource, artefact, etc but I don’t think you have to. If Dishonored never mentioned how electricity works it’d still have as strong a theme and mood as it does.
I don’t know if any of that was useful but I hope it was. It is by no means a silver bullet and might even be entirely throw-away but hopefully it does something. If you are still stuck, I might suggest trying a session or few of Journey, a journalling worldbuilding tool that uses some randomised prompts to get you to write about parts of your world, a process that was very inspirational and worked very well for me when I playtested it.
Lastly, I will re-iterate, my feedback hinges on “define your world more and why it is how it is” but if someone has another approach it’d be interesting to read about in the replies 
Good luck!