Actually, I was doing some research and I think the actual plugin to use is Meta_Plug_Morph. I have discovered it is a legacy plugin which means that you can use it for older scenes that were created in an older version. But, you need to add Meta_Plug first which is why this might not be the answer. Check in the help files in Layout>object Properties>Motion designer plugins. sorry I couldn't be of more help.
That other problem, I am not sure what you are doing, but it looks like you should use a particle emitter and you can attach objects to the particles. You can envelope the color channel of the surface to change the colors over time. I hope that makes sense to you. I believe it will make management a bit easier and you can still control the paths of the particles also
