Shouldn't matter. That extra connection is only used when power is needed. It's not going to push any excess power through the board or CPU.

Your higher temps are simply because you are dumping more heat into the loop. If you really think the rads are under performing you might have an air bubble. You could try tipping the case over in a different orientation.

Also you may want to add a flow meter. Perhaps your pump is having issues or you have too much restriction for the pump to overcome.