Made some notes I took after watching your edits a few times. Hope you don’t mind me sharing here!

Overall, I don’t think I noticed any technical issues at all.
I did notice a little bit of the original music bleeding through at the beginning of episode 2, when Cassian has the headphones on and is heading the rebel chatter inside the U-Wing. May be unnoticeable to most, I’ve just watched this scene a lot and recognize the music.
When I rewatched episode 1 on my phone at max volume, I noticed the sound of bats chirping a lot during in the scenes at Saw’s base. Sort of noticeable/distracting but not terrible.
I feel like the added shots during the rebel briefing do stick out a little.
I am overall impressed by your music choices. I thought the music choice when Jyn and Cassian arrived to Jedha was pretty inspired, since the music has a slight “Arabia” vibe, which is appropriate considered Jedha was filmed in Wadi Rum. I also really loved the music choices for Galen’s death, and Cassian’s speech till the end of that episode. Really great.
I don’t know if Mon Mothma really has a “theme” in the Season 1 Soundtrack, but I think having a track like that play when Bail and Mon speak would be an appropriate place to have it play. The scene feels a little incomplete with no music at all.
I think you’ve done an impressive job emulating the original score with Brittell’s work at times, and overall giving it the Andor vibe. I will say that I initially felt some of the music choices didn’t have the same “emotional weight” as the original tracks, like Your Father Would be Proud. I have rewatched bits and pieces of the episodes on my phone during and those moments that initially had less impact than the theatrical have grown on me more.
I do believe it might be better if this edit was “final” until after Andor Season 2, in case more favorable music options become available, or other plot details arise that may need to be straightened in the off chance there are any discrepancies.
It did seem like the new SFX when Jyn turns her head back and forth while walking away from Chirrut the first time they meet seemed a little loud.
I may be wrong but I think I noticed you re-inserted Chirrut’s line, “Is your foot alright?” between V1 and V2. I don’t have strong feelings either way about it but I’m curious why you decided to add it back in.
Also, I wonder if Chirrut’s staff hitting the troopers could be given a little more umph here and there. Sometimes it sounds like he is tapping them pretty lightly instead of hitting them so hard he is knocking them out.
Not necessary, but since we see a crashed X-Wing in the city but no context for it, maybe you could add some subtle X-Wing and TIE Fighter sounds during the street skirmish to at least set it up subtly.
You may interested, but I know there is an unused shot of the little girl Jyn saved looking up in the sky when the Star Destroyer is leaving that you could re-add to this version of the film if you wanted. There are a few other unused shots that could be useful here and there as well.
An opportunity for this edit: In the Partisan prison cell, Cassian says, “This is the first for me” in regards to being “worst cages than this”. This feels a little contradictory knowing that he has been in some pretty bad cages. You could argue he is being deceptive about his past, or being sarcastic, but I feel like with the added context of Andor, it would be better to alter this line to, “This isn’t the first for me” if possible.
I think if this was a movie edit, I would suggest removing all Bodhi scenes before Cassian finds him (and you removed all but one already), but with this episode format I wonder how it would feel if the following Bodhi scene when he meets Saw was back-to-back with his first scene. You could still cut the Bor Gullet scene, but maybe you could subtitle Saw when he says Bor Gullet, and it could mean, “Torture him.” Or something like that, to explain why Bodhi is in a daze when Cassian finds him.

Anyway, excellent work. This is like a dream come true honestly. I’m so happy you put in all of this effort to make this.

If you’re interested, here is a brief bullet point synopsis of the story changes I was planning to make:

Jyn wasn’t abandoned by Saw. She abandoned him (and the Rebellion). This creates a stronger juxtaposition between Jyn and Cassian’s characters.

The Rebels don’t know Bodhi was sent by Galen. They know about Galen’s involvement with the Death Star project, but all they know about the pilot is that he is a whistleblower that might have evidence of the project. Jyn’s initial mission is just to rescue the pilot, not find her father.

The Rebels offer Jyn a brand new identity so she can restart her life with a clean slate if she agrees to the mission.

A new dream sequence during the trip to Jedha showing flashes of Jyn’s time with Saw’s rebels establishing their questionable methods.

Chirrut “senses” Jyn rescuing the local girl during the Jedha City skirmish, establishing a clearer reason why Chirrut chooses to save them a few scenes later.

Jyn reveals that the last time Saw saw her was when he gave her orders to kill an Imperial officer’s family.

Galen’s message is now a “reveal” because we didn’t know he had sent the pilot.

At the end of the message, the hologram starts to become distorted and we don’t hear the name of the planet the Death Star plans are on.

When they’re rushing to leave Saw’s base, Cassian tells Baze/Chirrut they can come with them if they get the pilot while he finds Jyn.

On the U-Wing, we get a brief off-screen line or two from Bodhi and Baze establishing their motivations for joining the cause.

The crew is initially heading back to Yavin IV, but it is Jyn’s idea to find her father so they can find out where the Death Star plans are.

General Draven allows the change of plans, but now that they know the weapon works, he doesn’t trust Galen and orders Cassian to kill him.

Before he dies, Galen tells Jyn the plans are on Scarif.

On their approach to Yavin IV, repurpose Jyn holding her mother’s necklace on the stolen shuttle into a new sequence where Jyn remembers her mother and father (taken from Jyn’s original dream sequence from earlier), with some new elements to help establish her motivation for delivering her heartfelt speech to the Rebel Council in the following scene.

Potentially use cut shots of Cassian to establish him in the room listening while Jyn is speaking to the council.

During the Scarif battle, the only thing I would change would be that the Rogue One crew needs to tell the rebel fleet that they need to take down the shield gate AND lower their own shields in order to receive the transmission. Passing through energy shields would corrupt the data files. This makes all of the effort the crew makes into getting a signal to the fleet less redundant, since the fleet was already trying to take out the shield gate.

Make 2 endings: First, mostly the same but where we don’t see Darth Vader at all until the hallway scene. Second, no Vader hallway scene but we get one glimpse of his back. It also establishes that the disabled flagship is sending a transmission to another system and they’re tracking its trajectory. Movie ends where A New Hope begins.

I have mapped out already how I would make these changes work (with new lines, for example, some would be AI generated while others would be unused lines or frankenbites). I also have some ideas of useful alternative shots that could be used throughout the film. I can totally understand if you want keep this edit pretty similar to the original film beyond a few trims, but I’d love get a version of this with the music separate if you wouldn’t mind sharing.

Regardless, thanks for all of your hard work and sharing with us!