As a matter of fact, I have actually tried out quite a few different strategies for 5-2. I'll show you with this awesome picture I made in Paint:
If I say "square BC", I mean the square between B and C, I think you'll get the point.
As you thought, if I turn up directly when on square C and shoot the egg, I don't have time to push the emerald block into place and get to the bridge behind the snakey before he reappears. The same thing goes with squares A nd B, and all combination of these, if I shoot down the egg while it's down there, I don't have the time to get behind the snakey before he reappers, thus making it impossible to finish the level.
It is however possible to make it behind the snakey if I wait on the square between A and the heart, but if I am to do this, I would have to wait for the egg to reach that zone, and that takes to much time too. On the area named "not good either", it's not good either to turn up and shoot down the egg, the waiting time is too long.
One possible way of doing it is to walk directly from the "not good either" area, walk up to square D (in doing so pushing the emerald block up), turn right and shoot down the egg, and walk around the emerald block and putting it into place. If you do this you have time to get behind the snakey, however you don't have time to first push the upper snakey into the water first. This means that by doing that you have to walk directly behind the lower snakey after pushing the emerald block into place, shoot him and push him up, and after you pushed him up a bit, shoot down the upper snakey and push him into the water.
This leaves us to the last option, the way I do it in the fcm, directly walking around the emerald block, pushing it down one square and then turning right and shoot down the egg.
I guess I just could've said "my way is faster hanzou, that's just how it is" and you would have bought that, but being the scientist that I am I have to prove stuff :)
PS: If someone proves me wrong with this I would feel very owned after this big post about why my way was the fastest one! :)
EDIT:9-3 has now been improved by erasing that that one useless step:
http://dehacked.2y.net/microstorage.php/get/307/9-3new.fcm
This saved 26 frames.