Grievous capturing Even Piell at the beginning of Citadel might work! You could even go further and have Grievous outright kill Eeth Koth and capture Piell because of his usefulness. (Even if Koth appears in other episodes he could be said to be his convenient lookalike Agen Kolar, and honestly the fact he mades it to the early Jedi Purge in comics doesn’t really impact that much). I might watch both Grievous Intrigue and the beginning of Citadel to get some ideas running.

I’m not entirely sold on turning around the chronology of Revival and Younglings, mostly because I liked seeing a Separatist victory whose effect was felt later in the series. But in any case you have the last word, you’re right the Maul stuff should be rolling around as early as possible, and the original TV airing released those episodes out of order to begin with, so it’s a minor thing.

Your own feedback seems pretty complete, I agree with most of your notes and there doesn’t seem to be any issue that’s been oversighted. I think cutting the invisible witches sequence could work (maybe you could release alternate cuts?), and I agree with moving the Yoda and Obi scene to after Maul is restored.

For Assassin, maybe you could cut one of the visions or merge the two, this way it would feel more like a one-off, specific disturbance in the Force much like Luke’s unseen vision in Empire Strikes Back.