The Coaltongue incident was run mostly by-the-book, since the DM was not changing much then. Arkwright did change up the way the duchess and Sokana were introduced, how Sokana made it to the engine room, and how difficult it would be to repair the engine room.
Book #4, the train adventure, was among my favorite books. Arkwright presented the material therein reasonably faithfully, though expanded it with scenes and dialogue of their own creation.
I talked about this in another thread, but the "reunification of Ber," as Lily Fae puts it, played more towards book #6's sidebar on shaming Bruse Shantus than actually playing along with his game. It definitely took some extrapolation of events, and the DM had to revamp several events and drop the railroad-building minigame entirely. Still, it was quite entertaining.
Roland Stanfield's betrayal was one of the more heavily-revised plot arcs in our DM's run. We felt that it did not make much sense as presented, particularly the nonsensical speech in book #9 and why the Flint lighthouse was even necessary in the first place. We were deeply confused by what the lighthouse was supposed to do, because the lighthouses' function was established back in book #7, and book #9 tossed that out of the window while simultaneously contradicting book #10's outcome of events. This entire plot arc is why I really, really prefer for magic in this type of "scientific" setting to have consistent rules. So this plot arc was entertaining, but I would say that it was despite what the book presented, not because of what the book presented.
Book #12 had the most amount of custom content from the DM thus far. More than half of it was custom content, or expanded content. The metaphysics behind the Gyre were confusing and did not make all that much sense, but the DM was diligent in filling in the gaps of the lore and creating many new planes of their own making. Book #12 has been a great testament to our DM's level of skill and commitment.
Due to our rather unique style of playing through this adventure path, we already know what book #13 is about: coming back to Lanjyr delayed by months, liberating a mind-controlled world from the Obscurati (with some planar lantern/lighthouse mechanics that do not actually make much sense compared to how they were established in previous books, and some vaguely-handwaved "Ghost-Council-stabilized" hiveminds), splitting up to rescue four or five key locations via duplicants (we will likely be skipping the duplicants part, since we can teleport around with ease due to the planar configuration), and performing the Axis Seal ritual while competing with Nicodemus. We will be revamping a fair bit of this.
We have also already reviewed the mechanics of the final battle as a group, and we are dreading how janky and nonsensical much of it is. The final battle, as presented to the DM, is very naïve and ambitious. It reads more like how the author would want a Zeitgeist movie's finale to play out, while completely neglecting the turn- and round-based structure of RPGs and woefully underestimating the capacities of a max-level party. This section was definitely written by someone imagining a more cinematic and "rule of cool" battle, rather than the way, say, the epic Living Forgotten Realms adventures pay meticulous detail to providing intriguing mechanical and tactical challenges to a high-level party. In all likelihood, we are probably going to rewrite the mechanics and flow of more than half of the final battle, preserving only a few key statistics blocks.
On top of that, the details of the Axis Seal ritual itself are confusing, like the inexplicable double-slotting of planar icons, or the levitating Axis Seal that contradicts how the colossus was design to set the seal back down. (Never mind that the book #10's plot thread of Borne 2.0 being built in Cherage was completely dropped.)
The epilogue scenes have been described as "weaksauce." We will most likely be discarding them in favor of custom-written epilogue scenes. We have been very ambitious in changing the world, shaking up the status quo, introducing new magics and technologies, and making contact with the inhabitants of distant worlds and stars, so more down-to-earth epilogue scenes likely are not going to suit our needs.
Book #13 still seems very promising, however, and it looks like an epic finale to the best adventure path that we have ever seen.
Again, if anyone has any questions for how we have been handling some things in our game, or some of the more puzzling features in the logs, I am free to offer some clarifications. For example, my character (mostly) drops the annoying speech habit some time into book #8, and we are so engaged in the tactical and mechanical side of 4e combat that during fights, our text-based roleplaying in the in-character channel tends to be on the sparser end.