Running into a bit a headache inducing issue and hoping someone has some advice. :)
 
So I was finally able to put my X99 Classified together after a veritable nightmare with the CryoRig R1 Ultimate heat-sink.

X99 Classified Rig (Still Updating): http://www.modsrigs.com/detail.aspx?BuildID=34198

For a breakdown of my components.  I haven't started Overclocking the cpu yet so voltages etc are at stock.  My first challenge was getting a card in the first PCI-E slot, I have temporarily replaced the CryoRig R1 Ultimate with an Archon IB-E X2 and while I have zero issues with RAM clearance the sides of the Archon are pointed like a triangle and were doing a fine job of preventing my card from getting into place.

Yet after much gnashing of teeth, I prevailed and  the GTX 470 popped into the PCIE slot.  There was much rejoicing, yay!  As I am using the 5820K, I followed the manual that came with the board and socketed my second GTX 470 into the 4th PCI-E slot to ensure it would at least get 8 lanes.

I linked the two cards together using the same SLI bridge they've been using for the last year without issues (in fact it's the same case as well) and booted up.

My card in the PCI-E Slot 1 is definitely getting x16 lanes, per the bios, but PCI-E Slot 4 shows as being empty.  Now this is odd to me because I would not be shocked if the first card had issues but the card that's free standing and had no problems socketing in?  That's rather bizarre.  The entire PCI-E slot shows empty in bios.

It should be noted the same thing occurred with the primary card in slot 2, as I was not sure I could get it into slot 1, so the computer has already been updated with the latest bios (1.06) and has the newest WHQL drivers from NVidia.  The PCI-E Slot just does not show anything in it.  If I had something else to test the slot with, I would, but unfortunately I do not.  My understanding is Slot 3 is disabled, due to the CPU being a 5820K, so that's off the books and the last PCI-E slot is off limits due to reduced lanes and the fact it is up against the metal bar for the case.

The card *is* getting power and responding to the power as well, I got down with a flash light and confirmed the fan spools up on it the moment the computer comes on just like my primary card, so power shouldn't be an issue.  My power supply is an Enermax Revolution85 ERV1050EWT 1050W and can be seen in my old system here:

http://www.modsrigs.com/detail.aspx?BuildID=20827

I've tried with 1 bridge, 2 bridges, flipped the bridges, pushed the bridges in and let the bridges stay popped up and out.  I even tried to hook up the Tri-SLI hard bridge that came with the mobo but it won't line up between the two cards.  It's almost like it expects the PCI-E lanes to be a tiny bit closer, yet it would overshoot if I shifted slots up one.  The only thing I can think is there are jumpers to disable the PCI-E slots on the board (Like in some previous EVGA boards) and I'm just missing them in the documentation, possible considering I was exhausted last night, but I don't recall seeing them mentioned in the manuals.
 
Any help would be greatly appreciated!

Side shot of case:


Close Ups between two cards (As close as I could get the shot this morning running out the door):  

1. 


2. 

zophar
NVM, I didn't update my browser for like an hour and didn't see you had found a solution.

I haven't solved it yet, I was just thanking him for the helpful reply. :)  I'll mark the solution as soon as I have one but I am at work right now so the more ideas for me to try out when I get home the better.
 
Thanks! :D

When the cards are tested individually, are they detected properly? In each of the PCI-e lanes you are trying to use for SLI? Process of elimination, my friend. 

edited: never mind.. I found it

Just to be certain, you are plugged into the 4th slot, not the third, I ask as the pics looks like it may be in the 3rd slot.
 
http://www.evga.com/support/manuals/files/151-HE-E999_Part1_v2.pdf  page 9 shows the breakdown, but I think you already read that, if not, here it is, I would try it in slot 2.  Also double check BIOS under Advanced - PCIe Configuration and make sure nothing is forced to say Gen1 or something that could be causing the problems.
 
Also, just to rule this out as well, have you tried flipping the BIOS switch and trying one of the other BIOS's?  It may be BIOS related too if you are not in PE3.

@Fiveby5 - you get good CPU temps with the ThermalRight Archon IB-E X2 cooler?  Thanks!
 

EVGA_JacobF
For 5820, please only use PCIE 1 or 2 and 1 and 4.

Absolutely Jacob - with a GTX 470 in PCIE 1 you simply cannot get to PCIE 2.  I'd end up crushing the card in PCIE1 up against the heatsink.  I'm just trying to figure out why the PCIE ports appears to be ignoring everything put in them at the moment.  I'll be trying to switch to a fresh bios when I get home and will update with some better pictures as well.

Here, the flash is on now so you can count the PCIE slots and see I'm in slot 4! :)
 
I'm back on bios 1.00 but still no detection of the second card unfortunately. 
 

 
As for the heatsink, it seems to be doing pretty good right now, beyond the fact it made PCIE Slot 1 almost inaccessible.
 
Forgive the Trial Version markers, as it expired a while ago and I just forgot to update it.  After buying all this hardware it's not #1 on my list right now.
 

 
 
Edit:  Okay after a fair bit of coaxing I got the card into PCIE slot 2.  It was immediately detected and SLI is now active. 
 
My only question is how much will this effect my performance as my understanding is slot 1 and 4 is 16 lanes / 8 lanes, while slot 1/2 is 8 lanes/8 lanes.
 
I'm about to go run some benches to test things out, just thought I would update. :)
 
 

thatKingKong
Something's not right.  You should be able to use PCIe slot #1 and #4 to get 16x and 8x.  What are your load temps with that cooler?  You're running on stock speed or OC (please post the speed and voltage)?  Thanks!
 

I will when I get home, I was running stock at the time of the post, I've followed Jacobs guide in the sticky to overclock the chip to 4.2 though I needed a slight bit more voltage to get it stable.  I will say this, the CPU is not running hot at all, I ran it under AIDA64 stress for 10 minutes just as a fast check and it never got over 64 Celsius.  Then I ran it through superpi 32m and it completed without issues, I haven't tried to manually downstep my timings on the ram yet, but off the top of my head I think it was 6m 54s for 32m.  I do have a fair bit of custom work in the case to allow air cool to a much larger degree than it normally would, especially with my Apartment never going above 68-70 degrees, but beyond that I'm impressed with the CPU itself.
 
The top card is getting to warm though in this configuration, say 6-7 degrees Celsius,  it's fine when running at stock but my overclocks which you can see on my other computers have been running stable on my P55 FTW for over 4-5 years.  I tried to mimic one of them and immediately timed out during 3DMark Firestrike as the guy is walking down the platform.  As I was just damn excited to have the system working again I halted my benchmarks temporarily just because I knew it was running other things at stock without any issues.
 
I will most likely be re-enabling the backup power supply tonight to make sure it's not a wattage based issue but the Enermax 1050 watts should be able to handle 2 470's and a not so crazy overclock, I had the backup there when I was getting serious about benchmarking a while ago and could afford to do these things.  Now a days my money is absorbed by this nasty thing called "Day to Day Life" ;)
 
I'll update this more when I get home.
 
Edit:
 
As promised, I got home and rewired in the supplementary power supply that I've been using off and on for some time now in my old rig.  I moved the cards back into a PCIE1/PCIE4 position and believe me when I tell you that I shredded my knuckles doing it.  The position of the release for the PCIE slot makes it impossible to release card 2 without releasing card 1.  Since there is no gap between the CPU and PCIE1, the release for card 1 requires removing the fans from the heatsink, and then forcing my fingers under the heatsink to get the release on card 1 down.  Anyways, long story short I started when I got home from work and I booted up then ran the stress test to post this.  All and all it took about 2 hours or so to get it reset like this due to the way the release is 100% blocked in a PCIE1/PCIE2 configuration; then add-in rewiring the supplementary PSU and cleaning up the wires.
 
I reset the bios and booted up but once again PCIE4 is not detected.  We can rule out the card at this point as it worked fine in SLI all weekend in PCIE2 but as you stated it was x8/x8 lanes as opposed to x16/x8 lanes like 1/4 would provide.  I can't imagine what would cause that and all PCIE dipswitches are thrown to on.  Needless to say if I put the card back into PCIE2 I'm not going to be moving it again.  I can't afford to not have a computer right now so the idea of RMA'ing the board makes me extremely nervous, so if anyone has an idea on this, I would greatly appreciate it.
 
 
Attached is the stress test, I just used the AIDA64 one and ran it for 5 minutes, I didn't want to embed a huge image.  Yes I know it's short but I have to use the computer for work reasons right now more than gaming sadly, so I can't just sit by while it runs through.  It never got above 67 degrees Celsius and I've included the voltages and E-Leet in the screenshot so that you can review them.  I bumped the voltage up a little because I was running into freezing issues randomly but once I increased the voltage to the CPU it has not frozen a single time and temps have been just fine.

On the bios select the PCI-E as Gen 2