Now I'm trying to convert
The Tengu Conspiracy to 2.0 in an attempt to learn, and I'm still failing horribly. I just can't match up the obvious plot points to objectives as written, and it's torturing. If I can't do this, I might as well just give up any hope of GCing.

Does anyone have any clues as to what I'm doing wrong? Do the 2.0 LSpy missions bear no relation to mission design as printed, and I'm just spoiled?
Well, the first thing you really need to keep in mind is that the only thing the objectives is used for is to award XP--and a minor chunk at that. So don't sweat the details.
Next, consider the text that talks about objectives under the skeleton on page 430. Basically, assign 1-3 objectives per scene. Walk though the scenes and decide what the objectives are.
Look at the scene summaries for the tengu conspiracy. (Spoilers)
Scene One: The Butterfly involves the group trying to gain entrance to the Tokyo precinct house and Kurata. The agents have several options here, up to and including combat. Ideally, however, they should extract Kurata without killing anyone. Once they free Kurata, they discover that he doesn't have the chip, but that he knows who does. He can take them to a techno-industrial bar in the Ginza district where he believes the thieves are located. Of course, Kurata doesn’t reveal his connection to the thieves, or his own intentions concerning the chip.It would be simplest to use the rescue guideline, but the text provides a bunch of skill check ways to get the prisoner out, you might call it a skill check or a combination of the two.
I think I'd give them credit for rescue-1 and crucial skill check-3 (it might only end up being in the ballpark of 2, but since the players have to conceive a plan, I think 3 works)
Dealing with Kurata - discovering his duplicity is not an objective, but I'd make sure to give his character the bald faced lie ability if you don't want the adventure to derail at that point.
So, scene 1: crucial skill check-3, rescue-1 (maybe 2).
Scene Two: Recovery involves the group entering the club and confronting the thieves that Kurata hired. The thieves aren’t expecting an attack, believing that Kurata acted alone and is now safely in jail. Kurata takes advantage of the distraction caused by the group’s assault to grab the chip and flee.The objective that the agents know is to get the chip. But really, the agents are being stool pidgeons here. The real objective is going to be to uncover Kurata, and that's scheduled to happen in Scene 3. Not in love with that structure, but I'd say just plan out the objectives as you think they would occur, and if the players get the drop on Kurata, so be it.
I'd call the objective
neutralize here. Call them trained non-military authorities: neutralize 3.
Scene Three: Mastermind involves the agents realizing that Kurata is the true mastermind behind the theft, and pursuing him to a shootout in a nearby subway station where more of his allies lie in wait.This is almost a direct segue from scene 2; if I was writing it, it'd be the same scene.
But let's move on: the action, as the adventure planned it, involves them noticing something is up with kurita and a chase scene. Call it crucial skill check - 2 (I'd not max out Kurata's ranks or give him special abilities here; you want players to notice) and crucial skill check 4 (dramatic conflict)
So, I get:
Scene 1: Crucial skill check-3, rescue-1
Scene 2: Neutralize-3
Scene 3: Crucial skill check-2, crucial skill check-4.
Then convert NPCs. I usually just eyeball the ones in the book, in the extra NPCs downloads, and mouthymerc's NPC thread over in the License to Improvise thread and adjust to taste.