I've got two of the exact same motherboard you have, and I'm running six cards each as well. Using Ubuntu 12.04.2 LTS. I can't really say anything about Windows vs Linux, I've only been mining in Linux.
Yes, you do need a presence short on the 3rd PCIe x1. I've got all my cards on x1 to x16 risers (even on x16 slots) and had to do the presence short on that last x1 slot and the x16 slot just under it.
There aren't any additional power lines on the longer PCIe slots, x16 won't have any more than x1 does. Take a look: http://en.wikipedia.org/wiki/PCI_Express#Pinout - all of the power pins are on the little section before the notch.
On my boards, I use three unmodified and three powered risers. With my powered ones though, I sever the +12V lines going to the motherboard so that it only pulls power from the molex. I actually have those powered risers powered off the second power supply.
If you don't sever the lines, you have to plug those molexes into the same power supply that's powering the motherboard.
1600 watts should be enough, I measured one of my rigs with a Kill-A-Watt at about 1500 watts with all six cards running (before playing with voltage). I actually over-spec my power supplies, each rig has two in the 900-1000 watt range.
There's a mining rig in your bathroom?
Now for the issue of PCIe slots, all three of my 16x slots handle non powered and powered extenders fine. my 1x slots one and two are good, but the third one I think might need a presence short, it was being picky. As far as powered extenders go, I was planning to do something like all the 16x powered(three) and 1x (three) non powered. This should be ok I think, or do pcie 1x pull less power through the board and would benefit more from a powered extender? And or should I just power extend all 6 of them?
Yes, you do need a presence short on the 3rd PCIe x1. I've got all my cards on x1 to x16 risers (even on x16 slots) and had to do the presence short on that last x1 slot and the x16 slot just under it.
There aren't any additional power lines on the longer PCIe slots, x16 won't have any more than x1 does. Take a look: http://en.wikipedia.org/wiki/PCI_Express#Pinout - all of the power pins are on the little section before the notch.
On my boards, I use three unmodified and three powered risers. With my powered ones though, I sever the +12V lines going to the motherboard so that it only pulls power from the molex. I actually have those powered risers powered off the second power supply.
If you don't sever the lines, you have to plug those molexes into the same power supply that's powering the motherboard.
Now do you think a 1600w 80 plus gold psu the Lepa one, that should be able to handle x6 cards just fine.
1600 watts should be enough, I measured one of my rigs with a Kill-A-Watt at about 1500 watts with all six cards running (before playing with voltage). I actually over-spec my power supplies, each rig has two in the 900-1000 watt range.
-my gf wrote this while staring at my rig sitting on the toilet
There's a mining rig in your bathroom?