@Simon - Skinning

I've been trying to skin my bacteria for a few hours and even after combining my mesh I find the objects float off the model when I go and test out the skinning. Not all of the objects do it, the eyes and teeth and spine on the top of the head are fine but I guess that could be because it's 100% on that joint? I've tried painting weights and smoothing the weights but for some reason it's not letting me paint on the spines or the glowing circles despite the fact I combined the mesh. I know I'm probably doing something silly wrong but it's really confusing me.