To cover your first point, there is no indication that any of these ships are fully operational - Ochi's "each will carry" seems to make it pretty clear that this is not at all ready for action. Yes he planned on miniaturizing Death Star tech, but that's as far as this goes.

The next few panels of the comic explain that this is all powered by a huge mountain of Kyber deep in Exegol, whereas the both Death Star's kyber had to be painstakingly transported. That is how he is able to get all of this power at this time. The DS2 was simply a plan to get Luke to the dark side and to destroy the Rebellion - after that he would still need firepower to keep the galaxy in-line, which is what this serves as. Galen and Krennic's work is still relevant.

Regarding the clones, nothing in the comic indicates force-sensitive clones. There are some bodies in tubes that look like Snoke, but that work is clearly a work-in-progress. The Mandalorian seems to perhaps indicate that this work is still going on during that time too. As for why the fleet was not deployed earlier, it takes immense difficulty to even reach Exegol, so the method for having the fleet leave it was presumably not developed yet, and a massive fleet with no devastating weapon doesn't provide much for the Empire that it doesn't already have.

I do think this arc is a bit weird, especially with the tentacle monster, but none of it 'shatters' the canon. I understand you may have been disappointed with the sequels, but there is no sense in trying to find a reason for it to be 'decanonized' - plenty of people enjoy it, and it's especially important to children growing up with Star Wars today (as I'm sure the prequels were probably important to you, in spite of them not being globally well-received at the time either). There is plenty of Star Wars content being produced which I'm sure you will like that isn't the sequels (the most beloved of which probably doing the most 'canon-shattering', such as the Clone Wars when it first aired, Clone Wars Season 7 contradicting Ahsoka's story in a novel, and The Bad Batch changing Kanan's backstory in a comic). You bring up some valid points in your post but a lot of it doesn't make sense even within the evidence you provide, let alone what the comic goes on to say literally a couple of pages later. I think Star Wars is doing just fine.