I would take out the GTX1080 and boot up the system using the onboard GPU and HDMI or DVI out. If that works, install the WiFi card in the x1 slot and see if the system will boot up like that. If that works then it's an issue between the card and slot as you suggested, if that doesn't work, you may have a busted WiFi card.
Wouldn't it be easier to go for another WiFi card? Perhaps a USB WiFi adapter?