Remove the side panel --> do the temps come down on the GPUs?
 
SLI normally causes the top GPU to run warmer
 
ACX cooler remove a lot of heat, unfortunately most of that heat is dumped into the case.  Your case fans must get the heat out of the case before the warmed air is sucked back into the GPU, starting a loop of warmer & warmer air recirculating through the GPU ----> GPU temps rising
 
What fan curve do you use with your GPU ?
 
What fans are installed in your case & at what speed ?  Do they blow In or Out ?
 
Air 540 case
 
 
Air cooled SLI GPU = Full tower case with great airflow in my book

Without the side panel, the temperature will drop only 3C (ambient temp is 25C). 
upper GPU use aggressive curve and lower GPU use custom 1:1 50C:50% 60C:60%...


Most of the fans are Noctua fans. 

 

Do me a favour and try that curve, all fans togheter... 030% - 030°C --- 050% - 060°C --- 070% - 070°C --- 100% - 080°C
 
Edit: + Is there a dust filter on your forward-fans? If possible, remove it. + Decrease (temporarily) the Power-Limit of your FTW3, you won't loose your stock-boost, but the cards will probably stay colder.

I removed both the side panel and front panel and dust filter. But your profile is quieter than the one I've been using, the result is 76C.
It seems like that I have to lower the power target from 117% to 100% thus the clock will go down.

Some cases require the side panels to be closed to have the air actually flow through the case. Otherwise, much of the intake will vent directly back out, and the exhaust will just suck fresh air as opposed to having it travel across components between them.

Increase the front intake airflow... to lower dust build up, you want to keep intake volume at slightly higher than exhaust volume. When exhaust is higher than intake, you usually end up sucking in air through cracks or other openings that are unfiltered. If you can't increase it... lower or remove the one rear exhaust. Better yet, since its a 140mm fan, move it to the lower front and replace the 120mm fan there.
 
In addition, too high a speed at the top, will pull all the incoming air up, before they get a chance to blow across the GPUs.

 
The top fans are mounted with radiator and they won't blow too much air because of the radiator slows most of the air flow. 
And the reason I mount a 120mm fan in the lower front panel is that only 120mm fan can blow the air into the space between GPUs. A 140mm fan's position is higher and makes less effective cooling. I've tried 140mm before, the upper GPU got higher temperature.
The overall airflow is good. The only thing needs to change is the small space between GPUS. Hot air is concentrated there.

SilentMarket
The top fans are mounted with radiator and they won't blow too much air because of the radiator slows most of the air flow. 
And the reason I mount a 120mm fan in the lower front panel is that only 120mm fan can blow the air into the space between GPUs. A 140mm fan's position is higher and makes less effective cooling. I've tried 140mm before, the upper GPU got higher temperature.
The overall airflow is good. The only thing needs to change is the small space between GPUS. Hot air is concentrated there.

Airflow is good? Doubtful. You said it yourself you have no positive airflow to the GPU. Because you don't have enough to believe it's positive, then you can't be sure the hot air being generated by the GPUs is actually being evacuated from the area.

Are your fans capable of more than 1500 rpm? If so, turn them up just shy of the noise being unbearable. Yes, while the radiators do slow down airflow from the fans, you still have more exhaust volume than intake.

Do a smoke test to prove either you or I being "right."

But ya know what, I'm done with this topic.

How many drives do you have? That's a pretty wide case. Seems like there should be enough room to get your HDDs out of the main compartment and to the back side, giving you more room to play with for the video cards. If you have 3 pcie x16/x8 slots can you use slot 1 & 3 and place one of those pci slot blower exhaust cards between the video cards? I know that may require a different SLI bridge but don't they make longer bridges for different configurations?

 
I'm going to take away the HDDs to the backroom and mount fans under the GPU to see the difference.
The 3rd slot has PC front panel connector and system panel connector in there. It blocks the way to insert the installation of lower GPU the size of FTW 1080Ti.
If I remove these connectors the PC won't be able to start by pushing the start button.

Both cards do 76°C or did they get higher? If not, you can make adjustments... try 080% - 070°C.
 
Powertarget: Strange... I did that with my Founders and the boost did not decrease.

 
Only the upper card has 76C and my original profile is 90% - 70C. 
The lower card never reaches beyond 64C.
If the power target is set at 100%. When the OSD shows that the GPU power reaches over 100%, the extra boost clock speed will decrease.
Today I swapped two 6TB hard drives below the GPU to the second room. Normally the drive is around 35-36C but after they are set in the second room, both of them rises to 46C. It's because of no fan in the second room and PSU increasing extra heat. At this point, it proves that the cooling in lower GPU is enough for itself and hard drive, but not enough to prevent upper GPU overheating.
 

SilentMarket
So the conclusion is that I just purchased 2 1080ti and they're very hot...literally.

They're 280W TDP GPU's, and with the power limit increased this goes even further, don't be surprised they run so warm in SLI.
Especially with these GPU's that aren't a blower style cooler it's important to have enough airflow.
Though it's worth noting that these coolers will probably be a lot less noisy than you'd have with most tunnel-design coolers, and they run pretty hot too under stress.
 
My friend has two FTW3's in SLI inside a HAF X case combined with H100i & noctua 3000RPM (running about 2000~) fans on a i7 5960x, case is inside a badly ventilated desk (before 680 4GB Classified tunnel-blower SLI).
The GPU's both use Precision XOC's aggressive fan curve, 80°C would mean 100% fan speed.
 
The temperatures have been like this when the ambient temperature was about 29-30°C in GTA V (2.5x scaling I think on 1600p):
Main GPU (top): 76°C - fan speed 96%~
Secondary GPU (below): 66°C - fan speed 86%~
 
Temperature with 35°C outside, so likely easily similar ambient temperature:
Main GPU: 79°C - fan speed 99%~
Secondary GPU: 70°C - fan speed 90%~
 
The GPU's still run above 1900Mhz, only 100% power target.
I wouldn't say there is anything wrong with your cards and they perform as expected.
EVGA also uses one of the best TIMs available on the market, which is Shin-Etsu, as confirmed by @EVGA_JacobF:
https://forums.evga.com/FindPost/2502704
This TIM is also used for example by Corsairs AIO watercoolers, so I wouldn't bother to replace the TIM.
 
About the boost clock, with the Pascal GPU's the GPU Boost 3.0 is even more sensitive to temperatures, so even if it can draw enough power you still would want it to run cooler to achieve higher boost clocks.
 
http://www.anandtech.com/show/10325/the-nvidia-geforce-gtx-1080-and-1070-founders-edition-review/15

To start, Pascal clockspeeds are much more temperature-dependent than on Maxwell 2 or Kepler. Kepler would drop a single bin at a specific temperature, and Maxwell 2 would sustain the same clockspeed throughout. However Pascal will drop its clockspeeds as the GPU warms up, regardless of whether it still has formal thermal and TDP headroom to spare. This happens by backing off both on the clockspeed at each individual voltage point, and backing off to lower voltage points altogether.

You did a lot. What's left is to change the thermal grease, buy a different case or live with a hoover...
 

 
Edit: + Change the cards, maybe the lower will stay colder on top.

 
I am thinking of buying a motherboard that supports 3 slot spacing SLI with at least x8 x8 to enable SLI since my Z97 motherboard is old and only support PCI X8X4X4, I tried to mount the second GPU at slot 3 but it doesn't work with SLI though the temp is super good because the 120mm just blow right between the GPUs into the 3 slot space.

Carbonshape
Do you got an i7 with a -K? Try to get that board: EVGA Z97 Classified. That's just options I'm talking about: That Mix is still a powerhouse! And maybe buy a different case, something like the Obsidian 750D airflow... + Don't forget to enjoy your cards!

 
Yes, the PC is mounted with i7-4790K OC at 4600MHz, it's upgraded from 2014 980 SLI build.
I just googled that the Z97 Classified has special SLI ability, very interesting. 
But the motherboard is out of stock everywhere..:(

Ouh Mr. SilentMarket! First, I did not force you to anything, sorry. But I think you made a wise move. Besides, I got an Z87-Classy which is a very decent board that never ever compromised me. In fact, it is the best board I ever had. Well, you gotta assemble your stuff and if you do that right, there is NOTHING to worry about. You can write me via pm too, kind regards.
 
P.S. I know, the manual sucks. ^^ Contact the EVGA-dudes, I'm confident they will help you. - MAY THE FORCE BE WITH YOU
P.P.S. How's the condition of the board?
 
Edit:...

If this board is pcie 3.0 you really shouldn't see a performance difference between the x16 or x8 slots, so you should have a lot of options.

With pcie 2.0 yes you may have a small performance decrease using the x8 slots vs the x16 slots, so best to stick to the confirmed x16 slots if possible.