Ah, you are now talking about a subject that I have been preaching about for three months: Long cards , not short cards, over the ECP v4 header in the #3 PCIe slot. If you don’t do anything before installing the second position card, you are heading for problems down the road.
 
This is the solution and it is best performed with the MB removed from the case so you can get best angles of view.
 
First, my results are based on trials with two GTX580s , like you have. I have also tried two GTX480s. There was very little difference.
The plan:  To place two cards in SLI, optimized for spacing/cooling. I chose RED PCIe slots #1 and #3.

 
 
The #1 slot card will fit w/o problems.
The second long card in PCIe slot #3 has three interferences; at least it did for me.
The three things to consider:
1)      Front Panel AUDIO header, only if you have backplates.
2)      The Front Panel header (PWR LED, RESET, PWRSW)
3)      The 16-pin (2x8) ECP v4 header
 
Front Panel Audio header, if you have backplates, the fix will require you to remove the back plate and grind out a small area ( .75 X .25 inch) which comes in contact with FP Audio Connector. Do not try and bend this header. 
 
 
 

Front Panel header (PWR LED, RESET, PWRSW): bend just the PWRSW pins using the connector, 15-20 degrees towards the back of the computer case. You will see if any other pins on that header also need this operation by looking with trial fits. For me, it was only necessary to bend the PWRSW header pins. Bending prevents the connectors from acting like rigid vertical support beams.
 

 

Last, but not least is the 16-pin (2x8) ECP v4 header: This is more tedious fix, but when done correctly, works perfectly.
- remove the pins from the connector shell after marking them for correct reassembly (careful) Do both RED and BLACK.
 

 

- With no more than two strokes, each in opposite directions, at a time across a medium metal file, abrade the top and bottom of the connector shell until the distance between the surfaces are the same dimension as the inserted pin. I forget exactly, but I think I removed 15mm from both ends measuring with calipers after each two-strokes.  This will give the wires the clearance needed to seat your long card without generating high back pressure on the PCIe locking dog, or latch. 
 
The photo below shows, after the mod, a credit card thickness of clearance for the wire to feed through.

 
Connecting to the header is a little more tricky now because all the designed-in self-centering is gone because of the modification. It's not a big deal, just wanted to mention that it will require more attention when lining up the pins.
 
Also, after installing the connector and before inserting the GPU, dress the red and black wires to lie as flat as possible across the top of the connector shell. They will develop memory and you won’t need to do this each time you remove the GPU cards.
 


Warning (IMHO): If you force the card down in this slot without modifying the ECP 4v connector shell, you could damage the GPU card tab and/or the MB connector, warp the MB and potentially force the cable insulation to migrate, exposing wire that may short over time.  
 
 

 

Hope this helps. It worked perfectly for me.
 
I'll ad pix later if you like