your vibrate tag is going to vibrate all the clones together because the same object and vibrate tag are being cloned so they will all share exactly the same motion (it would be more obvious if you have more clones to make the helix) – I’m assuming you will want a random jiggling for each clone rather than them all moving together . If so, remove the vibrate tag and use a Random Effector on the Cloner set the Random Mode to Noise or Turbulence. If the individual parts of the molecules are going to vibrate as well the vibrate tags would work on each part…
The xpresso isn’t going to work that way I think, the best way seems to be using object mode with the cloner then attach the clones to a helix spline – don’t know it the geometry’s right for your purposes – but that way the xpresso works.
10403_fixcloneproblem2.c4d.zip
back to the original colouring problem – one way to do it would be put lights inside the metaball sources and use a Backlight shader to color the metaball – that will clone properly (though some tweaking would be required to get the look right)
10404_proximalproblem2.c4d.zip