if you plug into the Mobo's graphics, you may as well take the card/cards out altogether, you aren't using them
and if your using the onboard, that means that its using up your ram, slowing your system down and stealing your Fps :P
your rig works great with cards plugged in and monitor plugged to the card yes?
its the rad mounting that is the issue here
leave the grapics alone, move the rad, make it go somewhere else or mount on a couple of leg brackets to get the clearance from the back of the case,
once you start watercooling, you are almost automatically inducted into the modding circles as well, because theres rarely a 'from the box' fits everyone solution, its your ingenuity and resourcefullness that makes it all happen,
Now Come on, post pictures hehe and we can start mounting your rad up