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Using 2 x GTX680s the 1st one is getting quite hot compared to card 2, If I move card 2 to a slot further away and I stop using the recommended PCIE slots 1 and 4 will SLI still work and what performance will I lose if I do that.
You must use PCIE1 slot, and skipping PCIE4 leaves you with PCIE5 and PCIE6. PCIE5 is an x4 slot, and PCIE6 is an x8 slot.
In theory, SLI should still work using slots PCIE1 and PCIE6, since x16 - x8 SLI configurations are possible. You'll need a long SLI bridge to connect the two cards when using the PCIE1 and PCIE6 slots.
Performance wise, I can't give you an answer. I don't use that video card, and your question is so general, no monitor resolution given or games even mentioned.
Working on cooling the upper card is another option. I bet your H60 is mounted in the top rear fan spot, and configured to pull air in from outside the case. That leaves the one 200mm fan at the top as the only exhaust fan in the entire case! That is the main problem you have, all the heat from your video cards is not being removed from the case.
I've used two cases with 200mm fans. If a 200mm fans must pull air through a fan grill, they perform from fair to worthless. The same 200mm fan pushing air through a fan grill is not much if any better. They only work well with no restrictions, which one of the cases I had did have for the top fan. The side 200mm fan on a Corsair 500R case, pulling through a grill, was so worthless moving air it was nothing more than a LED mounting device. A single 120mm fan in the same location moved much more air.
I don't know what other fan mounting options you have for fans in that case, but I would check that. There are some new, better 200mm fans available, like the new Thermaltake models. I bet if you removed the side panel of that case and then played some games, your video card temperatures would be lower.
Thanks for the comprehensive reply. There is a 200mm side fan on the case which currently blows in, I think it would be better to reverse that and the top fan so that air is pulled in at the top past the video cards and out the side.
I can't find an SLI bridge longer than 120mm which is not quite enough to connect between slot 1 and 6. Are there any? Slot 6 also gets quite close to my bottom fitted PSU.
I did think of fitting 2 x Arctic Accelero Hybrid II and fitting the rad/fan units in place of the top 200mm fan.
I can see a new CPU and motherboard like the Z97 OC Formula but then I'd need anew CPU too.
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