I am using two GPUs in Slot 1 and 3. I have an M.2 drive in the M.2 slot. I also have another M.2 on a pci-e card.
If I put that card in slot 2 I get the following: x16, x4, x8
If I put that card in slot 4 I get the following: x8, x16, x4
It kinda sux cause the older Rampage V Extreme would give me x16, x4, x16 or x16, x16, x4 with no issues. I have never used a u.2 slot.
Without the PCI-e M.2 I get x16, x16 and the m.2 runs at x4. If I don't include the M.2 slot and just use the PCI-e I get the x16, x4, x8 or x8, x16, x4.
It is really unfortunate that the design of this motherboard is different from the original. That being said, I probably won't notice the difference between x8 and x16 on the GPU.
Panteks Enthoo Elite / Asus x299 Rampage VI Extreme / Intel I9-7900X / Corsair Dominator RGB 3200MHz
MSI GTX 1080 TI / 2x Intel 900p / Samsung 970 Pro 512GB
Samsung 850 PRO 512GB / Western Digital Gold 8TB HD
Corsair AX 1200i / Corsair Platinum K95 / Asus Chakram
Acer XB321HK 4k, IPS, G-sync Monitor / Water Cooled / Asus G571JT Laptop