Malevolence nitpicks:

Again, Padawan gets a capital letter, for some reason.
Interestingly, this time around you’ve done the opposite with the intro transition, having the episode audio come in before the picture does. I think it could be slightly more gradual, but I understand that the music is tough and the usable footage is limited because of originally having the newsreel audio.
At 2:15 you have a stray frame from a different shot.
Ditto at 3:22, we see a single frame of Plo Koon in his cockpit.
The audio cut on the word ‘worse’ and the fade at 7:44 is odd, like the show is cutting to commercials and back or something.
Similar for the fade after the cut at 8:10. Is this a footage limitation or something you added?
Again, a fade at 16:46; are these necessary to make up for missing footage?
The audio cuts out too early at 17:20.
I hadn’t even realised you’d replaced Plo’s dialogue until Ahsoka abruptly cuts him off mid-sentence for a hug. I quite like intercutting Plo’s dialogue with the clones getting ioned, but Ahsoka just butting in out of nowhere doesn’t really work for me. The footage reversal for the wipe is also not subtle.
At 18:28 when Yularen says “Skywalker”, the audio editing seems a little odd, like the music suddenly lowers (presumably to mute whatever Ahsoka is mouthing) and then it comes back in.
I hear voice echoes at 29:11.
At 29:23, Anakin looks like he’s about to say something else and it’s a little odd that he doesn’t.
I think Plo starts speaking too soon/abruptly at 29:40.

I’m enjoying this excuse to rewatch TCW and engage with it a little more than I did the first time. I don’t really remember the original episodes, but this edit makes a pretty fun short movie. You’ve merged the episodes well. The start is really engaging, as it quickly makes Grievous seem brutal and coherently sets up the threat. The medical station scenes work cleanly where you’ve put them. All the Plo Koon rescuing stuff is enjoyable enough - Anakin and Ahsoka’s interactions are exactly the sort of set-up I did feel was needed for the nitpicks I mentioned in my last post; and even though we haven’t seen lots of Anakin/Ahsoka missions, this episode does a good job implying there’s been a few offscreen.

The Shadow Squadron space battle section is watchable but not my favourite aspect of Star Wars. Whatever editing you did in this bit worked for me, though I can’t say I recall how it was originally. I was freaking out wondering how you’d managed to drag another thirty minutes of episode out after the Malevolence blew up but thankfully it’s just an accidentally left in black screen, haha.

Re: Cloak of Darkness - Though I see what you’re saying about it being more interesting for Anakin to palm Ahsoka off to Unduli and then later actually accept her in Malevolence, I’m not sure it really does that much for Cloak of Darkness. To some extent I think that scene you mentioned from the end of the movie, “…you might just make it as mine”, already shows he’s warming up to her emotionally anyway. I get that Ahsoka is already quite Anakiny even without his influence, but the interrogation scene in Cloak still feels like something of an callback to Anakin interrogating Zam in AOTC to me. Delaying Cloak would also allow some more time between Ventress’ appearances for her to have heard about who Ahsoka is. Definitely just a matter of personal opinion, though, and luckily there’s not really anything preventing someone from watching these edits in a different order.