Did alot of testing today and got the following setup (for a 44 lane CPU), with the help of HWInfo...
Expansion Slots (32 CPU lanes in total / 4 via PCH))
PCIEX16_1 -> PCI Express x16 Bus (shares resources with no other slot)
PCIEX16_2 -> PCI Express x16/x8 Bus (switches 8 lanes to PCIEX16_3 if in use)
PCIEX4 -> PCI Express x4 via PCH
PCIEX16_3 -> PCI Express x8 (gets the 8 lanes from PCIEX16_2 C/D)
M.2 Slots (12 CPU lanes in total / 4 via PCH)
M2_1 Onboard (between PCIEX16_2 and PCIEX16_3) -> PCI Express 3.0 4x via PCH
M2_2 Onboard (between PCIEX16_1 and PCIEX16_2) -> PCI Express 3.0 4x via CPU
DIMM.2_1 Module -> PCI Express 3.0 4x via CPU
DIMM.2_2 Module -> PCI Express 3.0 4x via CPU
USB Ports Rear IO (all connected to Intel USB Root HUB, from Wifi down and counted away from mainboard)
4 x USB 3.0 Ports next to Wifi -> ASMedia ASM2074 Pt 4/3/2/1 USB 2.0 /ASM3074 Pt 4/3/2/1 USB 3.0 4-Port USB 3.0 Hub -> Root PT 2 / PT 18
2 x USB 3.0 Ports -> Intel USB Pt 8/7 USB 2.0 Pt 24/23 USB 3.0
4 x USB 3.0 Ports -> Intel USB Pt 6/5/4/3 USB 2.0 Pt 22/21/20/19 USB 3.0
2 x USB 3.1 Gen 2 Ports -> ASMedia ASM2142 PT 3/4 USB 2.0 PT 1/2 USB 3.x -> PCI Express 3.0 2x via PCH
USB Ports Onboard
USB910 USB 2.0 -> Intel USB Pt 9/10 USB 2.0
USB1314 USB 2.0 -> Intel USB Pt 13/14 USB 2.0
U31G1_E12 + U31G1_E34 USB 3.0 -> ASMedia ASM2074 Pt 1/2/3/4 USB 2.0 /ASM3074 Pt 1/2/3/4 USB 3.0 4-Port USB 3.0 Hub -> Root PT 1 / PT 17
U31G2_EC1 USB 3.1 Gen 2 -> ASMedia ASM2142 PT 3/4 USB 2.0 PT 1/2 USB 3.x -> PCI Express 3.0 2x via PCH
Further Components connected to the PCH next to SATA / Network / Audio
Aquantia AQC-107 10GB -> PCI Express 3.0 2x via PCH
Wifi should be here too, but it's disabled on my setup.
Have no U.2 to check how those are connected, but according to the manual it shares the lanes with M.2_2 connected to the CPU.
If I have time, I will create a block diagram 🙂
@Hopper64 You can get 16 lanes running in slot 2 only if you leave slot 3 empty.
Which riser cable did you get and doesn't it interfere with the cooler of the second graphics card?