I've run the top half of the sphere again and this is the result......
Splendid!!..... i bet that felt a whole lot better

Note my cutter seems to get very close to the sphere on the roughing toolpath, this was something I didn't expect and a potential problem, I presume this is solved using longer cutters?
not sure if i get what you are saying...
i cant see any rough cut marks through the last cut... if your having problems though you will have to stipulate at the CAM stage of your G-code production how much clearence you want between your rough cut and finish cut