Cloak of Darkness nitpicks:

Padawan usually gets a capital letter.
I feel like the intro music lasts for too long over the footage of the ship before any actual episode audio comes in.
Ahsoka going apeshit on Gunray in the interrogation feels like a very Anakin thing for her to do, but you don’t get the impression she’s spent very much time with him yet, so you can’t really read it as his influence.
“Skywalker’s not here to save you now!” isn’t a reference to anything, right, because this is their first meeting? Again, seems a little premature, unless you can justify it as her referring to the events of Christophsis.
Ditto for “Master Skywalker should be proud”.
The end credits transition is really smooth here, but the long black screen is a little offputting. I can’t think of how’d you fix that though. Fade out slower? I assume the footage doesn’t allow it.

Any edits you’ve made to the actual contents of the episode are seamless!

While your idea to have Anakin immediately palm Ahsoka off is an amusing one, I think there’s just too many little references in this episode to Ahsoka being Anakin’s Padawan for it to work perfectly. If anything, perhaps this episode would be better placed a bit later so we can interpret it as Anakin’s unorthodox style rubbing off on her a little.

There’s some odd dialogue in these early episodes, haha. Ahsoka’s not that bad in your cut of Christophsis but she’s pretty chronic in this one: “hairless harpy”, “bog witch”, etc. Harsh words for a woman she’s never even met! I think someone else observed earlier that Ahsoka also doesn’t have any hair. I’m not at all advocating for cutting it though, because watching her become less snippy is sort of the point.

Definitely an essential episode for establishing Ventress, so it’s unfortunate that very little else interesting occurs besides Argyus’ betrayal (and death lol). Luminara Unduli is a really wooden character here, effortlessly slotting right into that humourless, overly-arrogant Jedi master archetype, to the point where Ahsoka doesn’t even learn anything this episode. Gree getting clunked while monologuing is hilarious though.