Have you tried a fresh install of the game?
Seems an unexplainable issue if your drivers are up to date.
My single 290X performs better than your 980's SLI so something is deffo wrong.
Hey fokes, Am using low FPS issues with Dying light.
Processor: Intel(R) Core(TM) i7-4790K CPU @ 4.00GHz (8 CPUs), ~4.7Ghz
GPUS : 2 X 980s watercooled.
Windows 8.1
Sli and Non SLI make zero dent in FPS, Am going to go with it's "Just the game that's broken" however checking google a lot of people claim that the main issue is there computer isn't good enough for it. Clearly mines is.
My FPS range from 20 fps to 60fps, Jumping a lot.
I also run G-sync but never really changes if it's on or off.
The utilization on them cards is so low, Have you tried forcing it into fullscreen, i have this issue on assetto corsa it looks full screen ( i think it's called borderless fullscreen? ) and i get 70fps ish and like 40% card use when i alt + enter i get 99% card use and 144fps :/ worth a shot?
What's it like with a single card? Might be worth trying of you get sick of troubleshooting and just want to play it.
Clean Build
Have you tried Revo Uninstaller? It's very good at locating remaining files once the uninstall process has completed. It may also be worth looking at CCleaner!