Just a few quick observations inspired by your post which was enjoyable and thought provoking as always. As you said the epi was neither a pure filler nor a thriller, just limping along towards more interesting ends.
For a background, while most of my friends here are ecstatic about JoJa fighting their enemies together and Jalal romancing her on the battlefield, I have been a silent contrarian on that. Everything may be fair in love and war, but everything is not the same in love and war. :) This was not the time for these two super-trained fighters to prove how much better they were than minimum-wage sipahis; it was the time to show responsibility, minimize risk, and maximize gains. I am not saying that they should refuse a fight forced on them, nor that Jalal should treat Jo like a doll and fight by himself. Instead, he should realize that killing poor peasant sipahis accomplishes nothing; he needs a few prisoners to extract information, and the two of them can only kill, not take prisoners. While they had a chance, they should have retreated and had the whole area surrounded by a large number of soldiers. That's how you take prisoners.
Of course, Mughal empire is not very good at investigating. Recall how Jo and Ja kept missing each other from a few feet away in Mathura? After MA admitted in her blast that she had hatched other conspiracies against Jo, Jalal ddn't even ask what those were! This time nobody thought of locking up palace gates, so at least they could track in and out movements (that would have netted Adham)---Maham, the only sharp mind in Agra, had done precisely that in Sujamal track, which is how Moti and Jo's outings got caught. Also no massive army was sent to the forest, which too might have netted Adham. We had more important things to do like placating Ruq. :)
So imagine my surprise that Atga did something right. I am not sure what purpose the lash served in DEK; these guys are warriors, haven't they seen a dead body before? Also, there must have been hidden refrigeration facilities in Agra for the body to be in such good shape the next day. :) Nevertheless, other opportunities already bungled, it was the only clue left and Atga did investigate correctly. Identify the soldier, his employer Gazi Khan, and the latter's protector Raja Ram Chandra; use gun-boat diplomacy to force the Raja to surrender GK; some water-boarding or its 16th century equivalent and GK just might come clean about AK. :) So there is a path still left to the real culprit whether they successfully pursue it or not.
I find the Shehnaz character underwhelming so far. Her pagal act is kind of charming, but she becomes a true pagal for me when she is being serious.
How did Shehnaz recognize CB's portrait if she got separated as a baby? Why blame Jalal who wan't even born then? She can throw a knife towards Jalal but how will that help her in getting the Delhi throne and, more importantly, in keeping it? But then Agra is full of nut cases who think that if only Jalal would die, everyone will accept them as the Empreror or Empress.
As for Ruq, I am so bored with her that I have stopped watching, reading, or even thinking about her. :) Please forgive me. I am sure your analysis was insightful, but I skipped it. I won't even bother with bhandaphod when it happens. That track has managed to lose me completely.