Now onto Book 3 (I’m doing a hasty review through with fresh eyes): I know you want to keep Gideon’s presence high throughout the series, but I’d change his appearances in this one. You have him in two main sequences in this movie - the first being the Shadow Council scene (where we learn that the Imperial Remnants are coordinated, get some good context for wider plots including Thrawn, and have Gideon declare he wants to stamp out the Mandalorians), and the second being the tracker scene and Gideon talking about catching Mando and Grogu to continue their cloning.
I think both of these need a little shift, and will try to justify why. But firstly, let me address the fact that I don’t think we need Gideon to have a strong presence in this movie. Yes it’s nice to see him, and to keep him feeling like an overhanging threat. But, so long as each movie at least escalates that threat, I think that need is satisfied. Compare now to your current Book 5, where we don’t see Grogu in the movie until the very end, which leaves us on an interesting development. I think doing the same here would be fine - you still come away from this movie on a punchy note where the Gideon plot has escalated.
So, regarding the tracker plot, I know it’s used here currently to illustrate Gideon’s will and skill to hunt Grogu down. However, the plot about capturing Grogu and his clone relevance really doesn’t continue until your Book 4. I know you’re using it to make the Imperial presence on the Mon Calamari planet more of a trap, but to be honest I don’t think that quite sells, with the dialogue we have. I also don’t think it’s necessary - from Din’s perspective his whole storyline in this movie has been to find Mandalorians, something he finally does at the end. Personal stakes for Gideon don’t add much here (especially as the Imperial resistance is quite weak), so having them as a thorn in his side which helps ingratiate him to Bo Katan’s faction is plenty.
Secondly, regarding the Shadow Council plot, I think that would work better AFTER that Mandalorian-Imperial conflict, as the triggering act behind making Gideon then declare that the Mandalorians must be stamped out. That then leaves our episode on the nice punchy finale (Thrawn reveal, escalation and all), which leaves the threat now overhanging the future movies. It’s the Mandalorians directly striking at Imperials which makes it into a vendetta for Gideon. I would also, as some have suggested, trim the lines about requisitions, as they’ll take now three movies to pay off. (Boba and team have also destroyed the Imperial base on Nevarro, including Gideon’s clones, this movie, so he’s taken a double hit onscreen, further justifying his rage at the end.)
This way, you’d have a straightforward Din-Grogu adventure as they seek Mandalorians, with issues and false leads along the way (and nearly bumping into Boba again), with their actions ending up triggering an escalation of the conflict between Mandalorians and Imperials.
Then, in your Book 4, you could introduce “I’ve placed a tracker” and that subplot just after Mando leaves the planet with that ex-Imperial warlord. We know she’s got ties to Thrawn, and thus the Shadow Council, so it’s absolutely feasible that an Imperial spy could be operating there to report back to Gideon. The dialogue there would reinforce that Gideon wants Grogu - and then he’d strike immediately, on the very next planet, where Din finally meets Boba and the Imperials show up to kidnap Grogu. Again, I think that’s neater, and keeps each movie more focused. You could cut the two elements of the tracker scene around the one of Din on the Crest trying to get Grogu to grab the ball with the force.
A final note on moving the tracker scenes to the following movie - this new suggested ordering would now make more sense of the lines about Pershing’s cloning work being lost, since in this ordering, this discussion would follow the events of Din and co destroying the final Nevarro facility (including clones) the movie prior.