The answer is simple. Sherlock jumped from the ledge and was rushed into emergency surgery. Molly, who had access to drugs, administered a drug to Sherlock that would slow his heart to the point where machines wouldn't register it as beating anymore. Using her position in the morgue, she falsified paperwork and made it so Sherlock "died". Either that or a doctor was paid off, but I'm betting it was drugs. Don't forget, he asked Molly for help and told her he was going to die the night before.
There was no trickery with the jump, it was nothing to do with another dead body or Moriarty or the garbage truck or, as one of my friends laughably suggested, the dummy in Sherlock's flat or the cyclist. The cyclist only caused John to become disorientated and dizzy, something which would put off his senses and impair his ability to draw an accurate pulse.
The cyclist also caused people to become distracted from the very simple truth that he did jump and it was him who slammed into the pavement. They made people focus on the wrong thing so the right thing would be less apparent. Any idea that there was trickery surrounding the jump is an idiotic idea.
It wasn't that high of a drop, maybe 4 or 5 storey's and it was in front of a hospital. That fact makes the chances of survival a lot more likely. It's clearly obvious that he jumped off the ledge and there is no way he was holding anything or had any means of breaking his fall. The only explanation which answers all of the facts is that Molly assisted him after he was in the hospital.