All bearings and seals come out of whatever is getting coated. As far as the bolt holes go, that is personal preference. I always have the powder coat sprayed over all bolt holes. Then just go over them with a tap. If you plug the bolt holes the powder has a tendency of building up around the thread plug and leaving an inconstant coating. As far as the steering stem goes, remove the seal, bearing retainer(hex thing), bearing and the stem spacer. Just show the powder coat shop where the steering stem bearing goes, they will know what yo do from there.