Try slight pressure on back of GPU toward motherboard and boot computer while maintaining slight pressure. That slight lift starts migrating towards the back of the PCIe slot and may cause X0, X2, X4 and X8. Worth a try! Note: If you have GPUs in SLI you will only get X8. Do you have anything plugged into the PCIEX16_2 slot?
If you have nothing else populated you should be able to get X16.
All the drives go down the DMI bus.
Sounds like either something in the system agent peg port config is off. May not be the MOBO but the GPU. How does your card stack up against similar systems in 3D marks, not comparing to those running LN2 of course.
FWIW a 1080Ti doesnt saturate X8 anyhow. X16 wont gain anything. The 2080Ti was the first card to actually saturate X8 and gaining a little, like 6% with it at X16.