I'm not sure I fully understand what you are looking for. At first blush it seems you underestimate the enormity of what you are asking for someone else to do.
It is my opinion that you would be better served giving the characters choices about what they want to do if you feel that there is a "being lead around by the nose" quality. Cressida might say that there's something going on at the butcher's shop, but there's also news about a slew of "runaways of pretty girls" in some posh district. They can opt for either mission, and you'd have to create the "runaways" mission yourself, but it could be a way to introduce the Gray (Grey?) Maidens concept.
It's very hard to disguise the "being lead around by the nose quality" of any pre-designed game, because they can't possibly publish a tremendous list of things your party can choose from. They have to follow the course to some extent or the story is going to become lost.
The idea of the AP in my view is to provide you with an overarcing string of story line and plot points that hold a main story together, and it is up to each individual DM to fill in the "missing pieces" that give the party a sense of spontenaity and that their choices actually matter.
Personally, I use a lot of old Dungeon magazines to add to my games. Hurly and Burly have shown up as common pests (though I believe we're up to Hurly the Eight and Burly XI... Heh.) which is from an old Dungeon magazine where the adventurers are waylaid by a seemingly errant Roc that draws them into an old watchtower occupied by two big baddies.
I wish you luck.
I think they could. You'd have to advance the elements of the Urgathoan cult in my view, to make the invasion of their Plaguehold (for lack of a better term) the culmination of the whole thing.
Perhaps Chittersnap is the very source of the disease-like poison that was used to kill the King and is actually another devotee of Urgathoa whether the rest of Eel's End knows it or not.
Gaedran Lamm could have been hired to spread the diseased coins via the orphans (who are some of the first to fall sick this could even be the lead-in for the entire group "Go see why these known orphan-thieves from one part of town are all getting sick...") and is a further link to the Urgathoans.
Perhaps the PCs deliver the orphans to Dr. Davaulus only to discover they've unwittingly been delivering the very test subjects Davaulus needs at the end of the thing...
With just the above thoughts I can already see how you might expand these first two volumes into a nice tidy little stand-alone.
The final culminating scene might be when the PCs rally enough support behind their circumstancial evidence (or you could inject quite hard evidence) against the Queen and they topple her then and there.
I'm not entirely sure what you think you're missing to wrap these two into a tight package on their own.
Alternatively, you add side quests that they can take on or not. Nothing like refusing a mission or doing a mission your way to feel that surge of player agency. I did that with this one:
Go to COTCTA RIOT ENCOUNTER: FIRE!.
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They don't put the clues together in EoA, they are just told where to go by their contact, and it seems more a string of dungeoncrawls (with the exception of Eel's End negotiations, sure). This might make the players feel like the DM is leading them around by the nose. While SDttG and possibly EfOK have the City Campaign feel of running through alleys, solving crimes, dealing with secret organizations, wheeling and dealing with contacts, and saving the city, EoA doesn't feel that way, and I'm looking at the other parts of the AP and I hesitate to use them.
Not trying to start a debate, but this depends on many things, this biggest of which is how committed your players are to their characters. One of my groups just found the trail and ran like a bloodhound toward the target, while the second group, who is truer to their characters, wondered around the city before going to the meeting at the beginning, and didn't trust the fortune teller, thinking that she may be leading them into a trap, so they did their own investigation before going in, to the point that they knew the approximate number of Lamm's Lambs there, and had a plan on what to do to help them after.
The rooftop scene is likewise very interactive as written, and Nick even goes to pains at the end of the adventure to give you a less railroad-like answer to the execution.