The space he fell on the pavement was marked. My theory is that he fell into the truck or a matress laid out on the marked space (from where he was standing, John wouldn't be able to see if he did, there was a smaller building in front) he then pulled out a fake body (like he did for Irene) and left on the truck or as a pedestrian. The ciclist purposly hit Joihn to delay him so that he reached the place too late to see that. Molly either helped provide the body, blood samples or later in the morgue.
What intrigues me is the whole "out of character thing". Sherlock was crying, reaching out to Watson, lying, and jumping out of a rooftop...all of which are out of character for him...