Make a multi-part enemy

OK, so picture a rubix cube. This is basically the model I'm dealing with. I want it so that the player has to shoot the outside blocks of the rubix cube before they can destroy the center. My problem is with animating the cube.

To make it, I basically made 27 individual cubes, arranged them in a rubix formation, then gave each of them a rigid body, so my projectiles will have something to collide against. The problem is that they bounce off each other and spread apart, breaking the formation. So I tried enabling all constraints, and that worked, as they no longer split apart. So I moved on to animation to make it spin, and that is going horribly. I also want it to slowly come down along the Y axis till it reaches a certain point, then hold position.

Here is where the trouble starts. Animations can't seem to do Y only alterations, it jumps my model to the X and Z 0 positions when the animation starts. So I tried doing it by script, and that blew up because it won't move with the position constraints on. and as I've said, turning them off makes the cube fly apart.

Any suggestions?

(also on a side note, the animation to make it spin pauses for a second when it reaches the end of the animation. really annoying, if someone has a fix for that too, awesome, but I'm more interested in fixing the character itself at the moment)