Hello, sempix.
After you tested only installing the RTX4090 in the PCIEX16 (G5)_2 slot,
has the PCIEX16_2 link speed on the PCI Express Configuration page in the BIOS been adjusted to Gen4?

If it is auto or already Gen4 but still cannot run in X8, it is recommended that you you visit the ASUS Repair Center to have your device checked.
Thank you.