Manual Focus Stacking Experiment with 2 Layers

I undertook this experiment to follow up on a discussion with VisionLight in another thread, and to begin to get a feel for focus stacking:
http://forums.dpreview.com/forums/post/50546444
Photo 1 is the dried out carcass of a fly.  The wing-tips are out-of-focus.
SX30 @ F/5.6, F = 54.1 mm, infinite focus + Raynox 250
Since I had to zoom out to approximately 1/3 of full optical zoom to get the whole subject, the Raynox 150 would have been a better choice because of its greater depth of field and less parallax among the photos that are being merged.    


Photo 1: Fly carcass with out-of-focus wing tips

With all the camera settings the same, the camera was moved a fraction of a millimetre on macro rails to take Photo 2 with the wing tips in better focus.  In Photoshop Elements 9, I made Photo 2 into a layer above Photo 1.  I reduced the viewing opacity of Photo 2 to 50% in order to align it as well as possible with Photo 1.  I was surprised that there was significant parallax.  When the lower edges of the lower wing were reasonably well aligned, the top edges of the upper wing were not.  I should have aligned the two wings independently but I didn't, so the parallax errors are quite evident if you view Photo 1 and the final merged image alternately.  Nevertheless, if you are not too fussy about that, the merged image looks moderately successful.



Merged image: Parts of Photo 2 stacked on top of Photo 1

I spent about an hour on this experiment and it was tedious work to merge just two images, partially erasing edges so that the discontinuities would not be very obvious.  Most of the hairs in this case are reasonably well focused, but it is easy to imagine photos where each hair would have to be masked individually, and even different portions of the same hair.  I have concluded that manual stacking is too tedious to pursue further unless the subject is fairly smooth.
The following YouTube video shows how focus stacking in Photoshop CS is able to automatically select the in-focus parts of an irregular subject from multiple layers:

http://www.youtube.com/watch?v=FM7yUUmGMvE

That looks quite impressive in the video.  I assume that the software also corrects parallax errors too, but that is not obvious in the video.