I had this happen once after I delidded a CPU. Somehow I damaged the CPU.
Did your GPU ever run at 16x? If it did then did you delid your CPU after you saw the GPU run at 16x?
Also you are using alot of pcie lanes already :
M.2_1 Slot NVMe (Boot): Samsung 960 PRO 512GB M.2-2280
M.2_2 Slot NVMe (Games): Samsung 960 EVO 1TB M.2-2280
SATA_1- Used, WD Black 1TB
SATA_2 - Used, WD Black 1TB
SATA_3 - Used, Toshiba X300 5TB
Maybe you just saturate them all.
*I am not sure but the problem might be with you secondary m.2 drive that you use for games. If you have that running in x4 mode maybe there's not enough left for the GPU. See if you can run it in x2 mode, I don't think that will make any difference from game loading point anyhow.
There's settings in bios to adjust the speeds for PCIe lanes. Try to adjust them manually.