I'm really hoping that I missed a glaring configuration option but I would be extremely grateful for support with this issue.
 
My Z97 Classified has 2 EVGA 980 SCs in slots 1 and 4, which the manual says both support x16. I have no other PCIe slots populated, however slot 1's GPU reports x8 in the BIOS and in GPU-Z.
 
Here's what I've done to attempt to solve this:
 
1. Updated to BIOS version 2.04. This eliminated the Power Management 24pin/6pin option, but I do have the 6pin installed.
2. Physically disabled the DIP switches on the PCIe slots that aren't populated. 
3. Disabled internal sound card, SATA RAID, and mSATA. I don't use any of these.
4. Ensured no O/C was enabled. Still the case; I'm fully stock.
5. Ensured Primary Display was set to PEG and disabled internal graphics. 
6. Forced the PCIe Configuration for slots 1 and 4 to Gen3, just in case.
7. I tried 2 SLI bridges that came with the motherboard; the soft and the hard one. 
 
I tried each of these steps separately.
My i7 4790K supports 40 PCIe lanes so there's no reason here why both of these cards shouldn't run in 16x.
 
Thank you in advance for your advice!
 

 
 

My mistake. With PCH it supports 40 lanes. The motherboard should recognize that, no?

I see.... so I could run in 16/16 at PCIe 2.0. Which would explain why all the posts I saw from older boards talked about 16/16 support for, say, 690 SLI, but 3.0 is faster even in my configuration...
 
Thank you for explaining that to me! Very informative. 
 
Would you be able to tell me why the board is reporting slot 1 as 8x and slot 4 as 16x, and if this is accurate, how I might reverse these, since the first card is preferred by the system?

I swapped them but the BIOS still shows the same result; 8x in the first slot and 16x in the 4th. 
 
Interesting, whereas before GPU-Z showed the first card running at 8x 1.1, it now shows 8x 3.0, and both times it showed the second card as 16x 3.0.

I can't even get the display to come on in that configuration. I don't think I can do 2 and 4. I remember discussing this with someone at EVGA before... 

They no longer sell the 'Z97' Classified anymore. They do have the X99 Classified. I'll bet the K designation was a nod to certain chips being unable to be overclocked and EVGA's offer that the board would still support it. 
 
Either way, I think I'll as EVGA about this specific thing. I'm running their latest BIOS and it's still within warranty. I haven't had this board but about a year.

This was discussed long ago and the thread is gone. The manual is incorrect, in order to have both cards @ x16 you have to use slots 1 and 2. I purchased this board to use 1 and 4 for slot spacing for X16 since I didn't (at the time) want to water cool my cards. It was determined the the manual was wrong and it was going to be updated to reflect the correct X8/X16 slot configurations..................obviously it never was.
 
Slots 1 and 2= x16/x16
 
Slots 1 and 4= x8/x16
 
EDIT: Same photo, kept telling me image was too large......

Here is the thread about it. http://forums.evga.com/8x16x-not-16x16x-m2185490-p7.aspx
On page 7 you will get a great lesson of the problem.
Since you only have 16 PCI-E lanes on the CPU it will be expanded with PLX chip to fake 2 x16 lanes on 2 and 4 but ends up as 2 x8 at CPU.

I get best results with 1 and 3 . 1 at x8 direct on CPU and 3 as fake x16 through the PLX chip that's end up as x8 at CPU.
All will be at gen 3 if your GPU supports it. If not you could try to force gen 3 in BIOS on each lane settings.

To use a setup like that, you almost have to put your GPU's under water or have a very good airflow around the GPU's.
The best air cooling solution for GPU that are so tight is the reference hairblower style.
Most aftermarket aircooling solution will need at least 1 slot apart some even 2 to get best cooling effect.
 
EDIT
Did some test with with GPUz on one GTX 690 (2 GPU on same board) SLI on slot 1.
The render test says on start both is running at x16 3.0 but after a minute or two the second falls back to 1.1.
If I recall this right, it's normal if the second GPU is not geting so much workload and then drops back. 

Sajin
Slots 2 and 4 are now working? 

Apologies for the late response. Yes, apparently all configurations work. I just have to enter BIOS blindly and then reboot the first time I make a change. I think it's a monitor issue. ASUS ROG Swift. All my hardware is good!
 

LazySoft
Did some test with with GPUz on one GTX 690 (2 GPU on same board) SLI on slot 1.
The render test says on start both is running at x16 3.0 but after a minute or two the second falls back to 1.1.
If I recall this right, it's normal if the second GPU is not geting so much workload and then drops back. 

If you're running in slot 1, you aren't using the PLX chipset at all because slot 1 is electrically wired directly to the CPU. This is ideal in scenarios where only a single PCIe slot is required, however I have benched and now proven that 2 cards run better on the PLX than 1 on the CPU and the other on the PLX due to inefficiencies in how they communicate. If you're curious about this, research the chips on the Z97 Classified responsible for this process; the PEX8747 and the ASM1480. The former is the PCIe lane switch and the latter muxes/demuxes the channels.
 
Ideally I would run my cards in the recommended 2/4 slot configuration but as you pointed out and I complained about, non-blower style coolers really don't like the be stacked. Also, not the most attractive way to run 2 cards, right? I'm hitting 90C on the primary card in that config in a matter of minutes, whereas when I give the card room to breathe it usually peaks around 70C. Not cool.
 
But... I've come up with a partial solution which gives me decent results with this board, even if it doesn't give me the warm and fuzzy feeling that my system is configured exactly as it should be. I moved the cards to slots 2 and 6. The PLX only provides 8 lanes to slot 6 but because both cards are on the PLX and the primary card receives a greater bandwidth than the secondary card, performance is much better. Aside from significantly higher heaven scores, I see less skipping than in both previous configurations (1/4 and 2/4) and the cards can breathe. I'm lucky that my case apparently doesn't mind a dual slot card in the last slot despite only having 7 cutouts, so I was able to test this and ultimately keep the configuration.
 
 
 
If anything, it encouraged me to try a different configuration, so thank you to all!