(Borrowed text, attributed below...)
Every building in Shadowrun has a story. Not like a history of when it was built, but a plotline of what the players are going to encounter, broken up into little scenes.
For example, the scenes of a hundred-story skyscraper could be broken down into: The Lobby. The Ground Floor Security Offices. The Elevator Core. The Security Ambush. The CEO's Bodyguards. The Office of The Badass CEO What Is Secretly A Dragon. [Ed: we have links to real-life building plans and other Shadowrun map resources here.]
Perhaps there are alternate or extra-credit scenes such as: The Loading Docks. The Computer Core. The Stairwell. The Security Armory. The Vaults.
In each 'scene', you decide: why the players might go there, how they would get there, what their opposition would be, what they will receive in info and/or loot, why they might regret going there. For example, the elevators might get them quickly to the top, but can fall under outside control (hey, something for the decker to do). The loading docks are out of the way, but one of the guys on the dock has a passkey to speed them through a few doors, and uniforms the runners could steal. And so on.
Most of the hundred floors, the players don't care about. And since there isn't usually much reason for them to kill every security guard in the whole darn building, the GM can find ways to bypass lots of that. Again, the decker is useful there. ("The security cameras you can access indicate that there's not much interesting on the 57th floor.") Sure, make him roll for it, but don't make the rolls too hard!
If the mission is in fact to kill every mook in the building, 100 floors is going to be a lot of game evenings! Otherwise, you just leave breadcrumbs: reasons that the players will want to move to the next scene, in the form of plot coupons such as passcards and camera footage, or previous objectives. ("The prisoner you are hoping to interrogate is in a cell near the Vaults, and remember your fixer said that she'd pay top Yen for anything you could liberate from the Armory.")
The decking nodes are the same. Remember that in SR4, the decker is on the team and tends to hack individual obstacles as the team encounters them - you don't hack the whole building while the rest of the team waits, as you did in previous editions. (Best part of SR4, IMHO.) Make a few important ones, and lead the decker to them with hints, preparation, and the occasional die roll.
Having some extra scenes for both the team at large and the decker is a good idea as you mentioned. If they are absolutely determined to hit the 34th floor, have a generic scene ready where they take out some drones, or find some data that doesn't help the mission but is fence-able later. (Or sets up your next adventure…) Optionally, you can move one of your planned scenes to the 34th floor and act if it was there all along. (I once had to move an entire city to a different part of a D&D map thanks to stubborn players; but that's another story.)
Hopefully this is more helpful!