the configs have very less performance difference.
I would say go with cpu 1 config since it has 650ti whose dx11 performance is better than gtx560. So newer games will run better on gtx650ti. Also gtx650ti consumes less power
Yeah the two graphics cards are near enough identical in performance. The 560 has a very small performance lead, but nothing noticeable. Driver updates will probably close that gap anyway. I'd take the better processor (though those are also very close).