The bumps could be a result of many different things:
They may be present in the Sculpey, and just harder to see until it gets painted.
If you're brushing on the paint, it could be something on the surface of the item or in the bristles of the brush, or perhaps the paint needs to be thinned.
If you're spraying the paint on, it could be a reaction to dust or even skin oils on the figure, or possibly the humidity is trapping moisture in the paint as it is sprayed on.
So without being there and knowing exactly what's causing it, here is just some general advice...
Be sure to prep your surfaces before painting. You may wish to sand the Sculpey with a very fine-grit sandpaper. Whether you sand or not, make sure the surfaces to be painted are clean and dust-free. Rinsing them in soapy water is a good idea.
Wash your hands frequently when handling an item that is to be painted. The oils in your skin are constantly contaminating the prepped surface. I even know some people who wear latex gloves when painting, although I prefer not to.
If you're brushing on the paint, it's always better to do several thin coats than one thick one. Acrylic paints can be thinned with water, and are my medium of choice. Enamel paints will require a chemical paint thinner, which leads to more dangerous fumes to inhale, so please be careful. You've only got one set of lungs, so take care of them.
If you're spraying on the paint, it obviously MUST be done outdoors (unless for some reason you actually want chemical pneumonia, which I contracted once when using gold spray-paint to finish a stage set in a hurry... and believe me, you DON'T actually want chemical pneumonia!) But the outside temp and humidity do affect the spray-paint's behavior, so you just have to learn when it 'feels' optimal outside for painting. Too cold, the paint will go on thick. Too hot, it will stay tacky and melty for longer. Too moist outside, you're gonna get water inclusions as the paint goes through the air.
Hope these tips come in handy.
As for Gonzo's flower, I'll keep an eye open for one, but I don't think I have one loose by itself. Not sure what you might want to use for a substitute... I've considered just filling in the hole in the jacket left by removing the flower before, but never found a flexible material that worked in the rubbery jacket, to my satisfaction.
Alex