i have recently got a new motherboard and swapped everything over as you would, but now the way the pci slots are positioned and spaced on the board my gpu's (gtx 260 SLI) wont fit and leave a gap so my first gpu is literally touching the top of the one underneth which is making the top one 10C hotter as the fan it being blocked.
i was wondering is there a way i could just take the gpu case of and leave the heatsink on and attach a fan somehow i took the case of them both yesterday and applied new thermal paste, it seems to have decreased the temps a bit but i would still like both card to be running the same temps.
The cards shroud shouldn't be left off as it helps in cooling by directing air from fan over it's heat-sink & other parts of PCB.
You can position an additional fan directly over both cards for better air flow and take a pencil eraser & wedge it between cards to separate em being careful not to go to far (small gap is all you'll need to help air from additional fan to blow in there).
With a duel GPU set up its common for one card to run hotter than the other.
Edit forgot; You can also adjust the bottom cards fan speed higher in MSI's Afterburner or in RivaTuner.