1.) You have to adopt both DSDT-patches and SSDT-X299.aml to your build and system configuration by means of IROEG. You cannot just simply enable the DSDT-patches in the config.plist. Therefore, they are disabled by default. Before enabling the DSDT-patches you have to verify them by means of IOREG! The same states for the SSDT-X299 implementation!
Some of your PCI devices are not yet properly recognised, see e.g, GPU, Audio, USB and some unknown device! Your GPU is currently assigned to thunderbolt, this will never work.
2.) The Thunderbolt EX 3 will show up under PCI after it's proper implementation in the SSDT-X299.aml!
Please check and adopt all device path entries by means of IOREG and where applicable also the PCIe Slot entries in the SSDT-X299.aml!
If you just use one ATI GPU in slot one, the DSDT patch SL05 -> GFX0 still should be valid! But you have to use the ATI device definition of
@apfelnico instead of my NVIDIA device definition in the SSDT-X299.aml!
Your IPG graphs reflect what? IDLE CPU frequencies? If so, your XCPM configuration does not work yet properly. Did you enable Intel SpeedShift in your mobo bios?