Ok. I located the issue. First to clarify the PCIe configuration for this board. It has 3 onboard PCIe 3.0 x16 slots and 3 onboard PCIe 3.0 x1 slots. Of those slots, 2 of each were populated. x16_1 and x16_2 were populated with my GPUs, x1_1 and x1_2 were populated with Elgato HD60 Pro capture cards. This left x16_3 and x1_3 both unpopulated. My SSD drives were connected to SATA6G_2 and SATA6G_3. Each of the onboard M.2 slots is populated with a 2280 M.2 NVME drive each.
As previously mentioned, both populated SATA6G ports and both m.2 slots were functioning properly. Both of the PCIe 3.0 x1 slots were also performing properly. The issue that was being experienced involved a reduction in speed from x8 to x4 on PCIe 3.0 x16_2. After pouring over the manual, rechecking slot assignments, and looking up PCI lane alotment, I stumbled across the Hyper M.2 footnote. In this footnote, it indicated that when Hyper M.2 (separately sold card) is active, the PCIe 3.0 x16 slots perform in a 8/4/4 configuration. After a good bit of digging in the BIOS, I managed to locate the Hyper M.2 toggle and disabled it. GPU-Z is now showing both drives operating at their expected x8.
Side note: As suspected, now that both GPUs are running at the full x8 the SLI subsection is now displaying in Nvidia Control Panel.
TLDR: Disabled Hyper M.2 in BIOS and resolved issue.
