Sherlock was very specific that Watson should stand in a specific place - where he could be hit by the bike being ridden by a member of Sherlock's homeless network.

Sherlock jumped onto the truck full of garbage bags, which then pulled off. The body might just have been Moriarty's, which Watson mistook as Sherlock's because of his knock to the head. Or maybe Molly or a homeless person planted a fake body. Alternatively, we know that some kind of Sherlock "double" exists, because the little girl believed Sherlock was the one who kidnapped her. Maybe Moriarty had a Mission Impossible-style Sherlock mask, which was still in his pocket? Seems a bit convenient though.

The post-mortem was fudged by Molly in order to fake Sherlock's death - we already know that's possible because Irene Adler did it.