I really like that story and may just have to steal it for one of my future campaigns. Mostly, I'm going to agree with what Charybdis said, in particular about withholding information. Giving them a data set and hinting that it's important is often far more effective than actually telling them what it is. Besides making retcons easier, it also makes the item more mysterious and intriguing.
One thing, and this is strongly dependent on your players, would be story pacing. In the first campaign I GM'd, I had a single long overarching story, and the team never got any jobs that were not in some way related to this story. I learned from that campaign: don't do that. It makes the plotline monotonous and predictable, and the players will get bored of the story arc even if it's fantastic. Besides that, it's usually unrealistic that a group of runners would only do jobs that have to do with a particular happening.
Even worse was a similar problem in the game I was a player in before that, where the GM had written the story into a corner, with the Big Bad having grown too powerful for us to stop on our own, but the corp that had been interested in stopping him and backing us had backed out. The story ground to a halt, so the GM sent us on a couple of throwaway runs that suddenly felt really empty and bland without the story arc to back it up. The group (over my objections) was suddenly so "tired of Shadowrun" (in actuality, bored of a stalled story arc, IMO) that we switched to Pathfinder, which I later learned quite literally bores me to sleep, and I quit the group. The group has not yet and possibly never will return to Shadowrun. Moral of the story: vary your story arcs.
My strategy for this round of campaigns (which is working much better so far) is to have at least two story arcs running at any given time - the A-story is long term (in these campaigns those are Emergence and Ghost Cartels, which will occupy the team for a minimum of 10 runs) and very "big picture", and the B-story is smaller-scale, more personal, and shorter arc (with around 4 runs contributing to it). I alternate between the two arcs, and sprinkle in one-off fun romps every fourth or fifth run. This has several advantages:
1) Variety is the spice of life, and all that.
2) I always have the next mission in each story arc ready to go. If for whatever reason I suddenly can't run the planned adventure on a given night (say, an important PC's player had to work late, or if the players short-circuit the story somehow), it's trivial to jump to next week's run and resume the first story another night. With a single linear story arc, skipping run is usually just not possible.
3) Sometimes a story arc may go for two or more runs without involving the Matrix guy in a significant way, or the mage, or having any big combats. If you keep this is mind the B-story can be given a scene to keep that player occupied and feeling useful in the downtime.
One final note (and it's probably too late to incorporate this) is a technique for stretching out the revelation of plot points without making it boring. You can basically get 3 runs instead of one from the revelation of something (say, of the existence of the citywide Awakenator): first, you allude to its existence almost as a footnote; second, you have it be indirectly relevant to the story of the run; and third, you send the players directly against one. I lifted this from the adventure seeds for the first chapter of Emergence, but it can apply to any big story arc.
