Depending on how much Dynamics work you want to try, you could do n8show's suggestion with the spheres, change them all into passive objects, then wrap a cloth object around them as a kind of shrinkwrap. If you have access to nCloth in Maya 8.5 or 2008, this is fairly easy to set up. That would solve your vertex alignment problem, and still only be as hard to model as a bunch of spheres.
-Tony