I've downloaded both the tutorial package and your code. The code aspect looks fine. So looking over the model I see that your vertex groups are not well defined. When I select the Left_collarbone bone, left_upperarm, left_lowerarm I seem to be getting vertices from parts of the torso, head, etc... in the mix. I suspect that what your seeing with your funky shoulder stretch animation is that the collarbone is part of some other groupings and when exported the "weights" of the mesh are confused causing the bone to pull badly on the mesh. Try cleaning up the vertex groups and see if that helps. @lukasz1985 has the right idea, nice one! +1
P.S. Thanks for the link to the cool animation tutorials for Three.js :)