I’ve watched movies 1-4, and am loving this so far. As promised, some more detailed feedback.

As ever, this is all caveated by me thinking these are absolute great movies as-is, and already my archival versions.

Universal

You have an issue with crushed blacks - you’re losing detail in your dark sections at certain points. It’s most noticeable during the lights-off prison break content, night time fireside chats, and on Trask, the Mon Calamari moon. Either this is caused by the standard reason for crushed blacks, or it’s something related to your grading or upscaling.
For me, all movies have too many wipe transitions. The show uses a few of them per episode, but that adds up a lot when compiling them into a movie, making them stand out against the usual SW movie format of 0-3ish. I’d review this where possible - even removing ones from the original content if you’re able to make the music around them work smoothly.

Book 1

This appears in the original episode too, but IG-11 in his first appearance keeps referring to “said asset” having not mentioned what “said asset” is. It’s almost as if there was a cut line first. Editing that to have him just say “the asset” would fix this.
There’s a slightly awkward musical transition before the E-WEB (or whatever cannon) fires before Mando and IG find Grogu for the first time.
I wasn’t entirely clear on why Mando doesn’t have the blurrg for the return journey. Was there anything that showed him losing it?
Narratively it’s a bit odd that Mando enters the mudhorn cave on his walk back. I thought Smudger had a solution for this where Mando stumbles upon it just outside the cave, but you mention using Smudger’s idea there so you must have considered that. However, you could alternatively use one of the scenes where it just charges in and knocks him down, as a suprise introduction to that fight.
You might not need this with your new 1,2,6,3 structure, and there might not be any content here, but seeing the Imperials respond to Mando’s theft of Grogu in some way would be nice if possible.
When Mando starts the prison break episode content, you could cut the scenes where Mando shows off the razorcrest to the guy who sends them off on the mission (the guy who owns the station). It’s not vital to cover that “we just need your ship” subplot, instead just getting into the crew introductions. (If any of that dialogue is useful, it can probably be shifted to elsewhere as that segment is quite talky.)
I’d still vote for showing Mayfield and the others alive, perhaps before you return from episode 6 to episode 3, to show that this is a guy with morality, before we get into the Grogu’s carrier/Mando’s flashback sequence.
Potentially split Kuiil and IG into two scenes at different times in the movie - one where he’s recovered, one where he’s repaired - to help sell time passing.
There were a couple of nice shots in episode 2 of Mando admiring his ship, and a nice hero shot before it lifts off, which I think you cut from this movie. I’d keep them - if any movie deserves a ship hero shot, it’s your first.
You could cut the references to the Mandalorians needing to leave their culvert here, to make their empty nest a bit more of a darker suprise when they’re lost in your Book 3.

Book 2

If including the wetlands planet’s content here, I’d either go all in (and play most of the episode including the raider fight) or absolute minimum, focusing on the character drama. For the latter, I’d consider cutting the Cara Dune fight (you could potentially skip from Mando asking “who’s she?” to some Boba content, then back to Mando and Cara in conversation). I’d also remove the shots of Mando training the wetlanders in use of weapons during the montage if you’re not including the raider fight - if something’s needed in its place to preserve the music there, there must be plenty of passive wetlands shots you could use.
This is a silly note, but I love that now Boba gets his vision quest from the powder rather than the lizard, the scene plays out as “Here’s a lizard without context. Anyway, take some drugs.”
The first transition from Boba to Din does need a wipe transition, I think, and a little extension to let the moment breathe.
There’s a moment where you preserved the original Boba episodes’ ‘fading in and out of the Bacta dream’ graphic. This kind of worked as he was a bit fuzzy headed then, but it might be a bit neater if you can skip those bits.
The pacing around the overlap episode could be a little different. At present, there’s more from Boba that could be shifted toward the ‘present day’ and intercut with Mando’s story more. And equally, there’s a point in Mando’s story where the kid bounty hunter disappears, but then we cut very quickly to everyone being back in Mos Pelgo. I’d get some more Boba content (e.g. him and Fennec round the fire?) into that space, to give the others more implied time to travel back to Mos Pelgo. (Those Mos Pelgo scenes happen in the day too - why not have that be the next morning after the fireplace night?)
This is more a fault of the original, that it feels a bit weird that Fennec recovers away from the mod parlour, so she’s still out in the desert having apparently been taken to a facility that can repair her. There’s not much that can be done, perhaps, though I might just skip the ‘mod repair’ angle entirely, including removing her showing off her mechanical innards from Mando episode 14 too. (This might conflict with future content if her having cybernetics comes up in future though.)
The sarlacc pit to fire conversation wipe felt a little abrupt.
See previous notes about shifting some content between movies 1/2/3.

Book 3

I’d remove the guy giving Cara money without context. It raises too many questions.
Did you remove the expanded aspect ratio stuff from Mando episode 9 versus the Krayt Dragon? I think that was a lovely artistic touch, I’d preserve it if you could.
As much as I enjoyed it the first time round, for pacing and tension, I’d avoid the humorous scout scene conversation as much as possible. We need to feel that Din’s crew and Grogu need rescuing, so we need to get to IG doing both.
I could go for even more removal of Din not liking droids. It doesn’t serve much purpose.
With the move of the foundling flashback to Book 1, you can remove more of its references here.
I liked what you did throughout to hide Din’s face, but in that case, I’d not even tease it here. Watching the original, I felt like you could easily cut around having Mando need IG to take his helmet off, and just cut to a later point in the sewers when they’re all back together.
In the culvert, Cara has sensible dialogue saying “hurry up, we’re pursued by Imperials!” Problem is, it comes quite late in the conversation - I’d shift it to earlier in their conversation if possible.
The waving baby joke felt a little awkward, I’d remove that if possible.
The content from episode 8 ends on very ‘final’ feeling music - I’d soften this moment if possible. (Also see my earlier note about potentially moving eps 7/8 to Book 2, and opening Book 3 on episode 9.)
Ideally we cut the unnecessary Abyssian, which feels like too much of a reintroduction to Mando. If you do restructure these, You might be able to cut him out entirely for the opening of a Book 3 which starts here, and just assume Mando picked up a rumour. (I think in early dialogue he says “I heard there was a Mandalorian round here” or something.)
I found the Krayt dragon swimming through town to be a bit odd. Wouldn’t the infrastructure built on the sand collapse? I wonder if the earthquake would be sufficient, only revealing the beast’s scale when they go to attack it.
I’d cut the scene where Mando’s bike gets destroyed by some random pirates. Instead you could just show him travelling homeward, then cut to Mando walking with his pack and kit when he’s in town, presumably after having parked it. It didn’t quite track for me that it was set up by Boba - I’d stick with the original shot sequence for the Boba reveal.
I think Smudger created an alternative landing on Trask which avoided a lot of the damage to the ship, which could smooth that out for you - especially since we don’t now have an obvious cause for the damage.

Book 4

Very little to say here. Only real issue for me was the inclusion of episode 12. I like the episode well enough, but I think it’s not necessary and it gets in the way here. Whilst the reveal of the cloning facility is cool, it doesn’t tell us anything new (other content this movie tells us about Pershing’s work and wanting Grogu as a ‘donor’.), it has a few too many moments of goofy humour as part of the core plotline (so they’re uncuttable), and some of the action is a little weird too (the vehicle dropping from a massive height). In this context, it causes the movie (centered on getting Grogu to the Jedi, as set up by the last episode) it just slows us down. I think opening on Mando having arrived at Calodan, where he was sent at the end of Book 3, would be the stronger start. And hey, if people want this content, they can just watch the original episode in between both of your movies.
You could also, if you wanted to, include some of the ‘welcome to new Nevarro’ scenes with Greef and Cara, preceding the later scenes where Mando comes to recruit Cara.
Oh, and the tracker scene could come at the end of your previous movie now, since that features an Imperial presence.
You could probably also skip Cara being deputised, since she’s not going to appear again so that plotline won’t go anywhere. Now, she’s able to buy Mayfeld’s time through unknown (but not unimaginable) means, and then they cheekily don’t return him to the New Republic (which she’s no longer associated with).
Oh, and your v3 of Book 4 doesn’t finish playing the credits before the file ends - so I’m not sure if you include the Boba-on-the-throne stinger or not, though I’d recommend it here.
The Grogu with the wires scene is cute, but I felt like it felt a little chopped into place here.
I could have done with at least a little hint as to why Ahsoka is on Korvus, at least something to imply it’s deliberate to her and not just hanging out.
I do think your cuts to not show Din’s face work, though it comes off as quite deliberate direction that the director is now trying to avoid showing it to the audience, which took me out a little. I don’t know if this scene’s dialogue can be tightened to avoid some of the more ‘deliberate’/awkward shots? On the flipside, having Mando ‘naked’ would add to his vulnerability here, and therefore the tension of the scene.