Prey - you forget I'm on the same thread as you and so saw that Basil Rathbone story too, I even commented on it! Try harder! 
MadameOvary - yes I did!
Mushy - I thought you were going to be a huge die-hard fan yourself but now you've just made me look a little odd! 
Right. 8yr old ds has solved it for us. I knew there was a reason I called that boy Sherlock (and btw he has been telling all his friends about his unusual middle name and they all love it!)
Holmes asks Molly for help but we don't see how she helps him. He tells her he has to die. That means that she has to confirm that the body she examines in the morgue is Sherlock's. That's the favour.
On the rooftop, Sherlock told Moriarty "I am you" and this was repeated a few times. Of course Moriarty had a Holmes disguise - hence the girl screaming. Holmes knew this, how could he not know?
Just after Holmes fell, we see the truck that was parked there, drive off. Watson has been knocked out - how long for? Long enough for Moriarty's body, complete with Holmes disguise, has been laid out on the pavement - hence also the head wound. The body is then taken into the mortuary and is pronounced as that of Holmes by Molly. The funeral would have taken place etc but Moriarty would be in the grave, not Holmes.
Watson had to see Holmes die, he was the key witness. He was carefully positioned, the cyclist was planned. If Watson hadn't seen Holmes die then all three; Watson, Mrs Hudson and Lestrade would have been killed. As at Reichenbach Falls, Holmes had to let Watson believe he was dead or else Moriarty's henchmen would have come to finish him off and Watson himself would have been in danger.
Holmes puts his hands behind his back, he is concealing something. Perhaps the rubber ball that would stop his pulse? Perhaps that in itself was a signal?
There are continual references to illusion and magic tricks, the Make Believe art on the reporter's wall, the fact that the newspapers "tell the truth" - all of it was a big con to convince people of Holmes' death.
And did you note down the music Moriarty was playing on the rooftop? "Stayin' Alive" which is just what Holmes did.
Have I missed 'owt?
Credit to ds who spotted that they kept talking about Moriarty being Holmes on the rooftop. He had it sussed.