I do hope you've not finished this run, looks like epic goodtimes:)
May I suggest:
1: If someone's got a phone, and it goes off while you're playing, it goes off "In game". Someone, ages ago, had that rule while his newb players were checking out a coocooned spirit, and the noise woke it up...It's really horrible watching the "Ohshitohshitohshit" fumble to turn the phone off and runners screaming for the hills while the unlucky player is chased...
2: Misdirection and lies. You've already got a betrayal in place (fun, can be disheartening if not done right) why not 3 or 4? Get your people hired, or hint that they might want to find out more on their ownsome and sell the info to various interested parties, like that helpful fellow they know. Burn possible allies while helping the great dark evil...

3: Whispers on the streets and contacts disappearing/reappearing. If your players are White-wolf vets, they should cotton on fast that there's something not quite right.
4: Magic-users getting hints and tastes of something...odd, in the air. Play up weird feelings, then dismiss them as imagination.
5: Don't neglect the 2nd edition stuff, it was seriously well crafted and useable now. Yes, that includes the handouts for the UB.
6: Queen Euphoria is the classic, but don't forget Double Exposure. It's got misdirection galore and can cause TPK if your players don't think before acting. Also, it lays on the "everything is normal, there's nothing to be afraid of..." vibe. And if you do it right, you can simply let the bad guys be Renraku, testing their gear on the less fortunate. "Yep, job's done, those corp fraggers got what was coming to them, nothing else to see here"
7: Frankly, Euphoria would be best run last and then burst Bug City over them. ("You gottas get out of Seattle, it's too hot, too weird. Try the East coast, Boston, DC, wherever...") Mob contacts are good hooks for this sort, as is a interest in the electronic decking side of things. Magic too - their uni there was great pre-bug.
8: Bug City. Nightmare fuel, survivalism, escape. (Make them bleed here. A lot.)
9: Betrayal. Epic, epic betrayal. If you don't try and kill your players here, they won't respect you ever again.
10: Dice shower as your players work out you are an evil SOB. Then screams for more.
-Hope it runs well:) I can't do this thing to my players now, they're too wary. So I sideswipe them with voodoun, possession, evil magical threats and the ever-present horror of the Tax-man.
-Tir.