This is super long and probably repetitive, but anyway, this is my theory on how Sherlock survived (I typed it all out on a Word document, haha...):
- Sherlock and Molly devise a plan to fake Sherlock’s death. Sherlock has Molly find a corpse that has the same height and build as himself, makes a Sherlock-mask to fit the corpse with, and dresses it up like himself. They add the necessary blood and other effects to make it look as if Sherlock had really jumped and sustained a dreadful impact with the ground. She also provides Sherlock’s fake death certificate and covers for his post mortem examination.
- John arrives at the hospital and later receives a phone call from paramedics telling him that Mrs. Hudson has been shot. Sherlock does this so that John is lured away for enough time to allow Sherlock and Moriarty to solve their final problem up on the rooftop of St. Bartholomew’s Hospital.
- Sherlock has probably guessed what Moriarty has planned and plays accordingly in order to ensure his and his friends' survival. Even when Moriarty kills himself, Sherlock knows he must continue with his “death" to save his friends.
- When Sherlock and Moriarty look down, Moriarty notices some people below and mentions that Sherlock’s gotten himself an “audience.” This is, in fact, Sherlock’s homeless network (assuming that he's asked for their help) setting up the scene which also includes the truck that has parked in the front of the building.
- After Moriarty’s suicide, Sherlock steps onto the side of the rooftop, possibly to signal his homeless network to lay out the fake-Sherlock-corpse and a mattress (or something soft) in which he will soon land upon.
- John returns to the hospital after discovering that Mrs. Hudson is safe but is phoned by Sherlock. When John tries to get closer to the building, Sherlock firmly tells him to stand at a certain spot and stay where he is so that John does not see what is happening behind the truck. While they are talking, I think Sherlock tries to communicate to John that his death is fake, especially when he says that "it's just a magic trick." When Sherlock falls, the bus obscures the impact from John’s perspective, and John will be too shocked to run forward (Sherlock, after all, is the master of understanding human reactions).
- Sherlock must prove to John that he himself is really dead but knows that John is a doctor and can easily distinguish how a person who has just died and a corpse that has been dead for days feels like. So Sherlock has one of his homeless network pose as a bicyclist to deliberately knock John over to: 1) disorient him so that when John finally gets back up, he is too dazed to really take in what he sees and feels and 2) allow enough time for the homeless network to take away the mattress and allow Sherlock to drive away on the truck (as seen when John kneels next to the corpse the truck is already gone).
This whole day was really... depressing. I just kept thinking about the scene and everyone's reactions, especially John's. :( And how I am going to be slowly dying while waiting for Series 3 for Sherlock to show up again. Anyway, hope this helps!
Observation and lots of thinking. :)