Great JOb!!!!
This was very well made. This is an example of claymation at its best. The camera shots are really well done and the clay figures are well developed. The use of shadow and light is fantastic.
The compression of flash is omewhat limiting and this would be best done on real film, but this might also necessitate smoother motion and other improvements in lighting, clay modeling, etc.
The story is fine, very much in the vein of David Lynch's Eraserhead. Hard to fault this. The music also is perfect. I really can't find fault here, except to say that any problems are covered up by the low resolution of flash. To get better feedback, you will need to work in a higher resolution.
It seems you may have studied the animations of Jan Svankmeyer and the Brothers Quay already. If you have not, do so. You will find it instructive.