Question How to check if everything is running PCIe 4.0 or 3.0 ?

[ohm-ish]

Because you have not forced M.2 slot into gen4 mode.

In gen5 mode (or auto) M.2 slot is using PCIE lanes from CPU
(and just downgrades PCIE mode internally to gen4 because of gen4 drive)
Gpu slot has to be switched from x16 to x8, to accommodate that.

In forced gen4 mode M.2 slot is using PCIE lanes from chipset and gpu is free to use all x16 connectivity from available CPU PCIE lanes.

Ok
I looked in manual and found the way to force x16 for the graphics card in bios
And it works. Card now runs 4.0 x16.
And I checked the NVMe speed. it's the same as before I did this change