Here is a pastebin of the lspci output for the root port. I've done many things from cleaning PCIe ports to trying different graphics cards but nothing has worked. This is causing my primary and only graphics card to run at 8 lanes instead of 16. I have run out of ideas and come to the community for a larger mind!
I am kind of lost with the information you have provided so I will need to get more information on that.
Please provide me with the system information report or the dxdiag report. Also, Can you please tell me what is the Graphics card you have and the exact motherboard model?