I was able to get rid of most of them on the right hand side by picking up parts in BB view, moving them away and back.
Try to avoid parts on parts or wires on parts, ie see the green wire on the cap top right, it's probably not connected, put the wire in front of the cap.
I was left with the VR and PWR+1 header rats, which I couldn't delete, so I duplicated them, deleted the originals, and moved the duplicates into place.