@Shadowbane Thank you for your response. I took some time to figure stuff out before hastily leaving a reply and also to see if I can fix this issue. First of all, when you say you passed my query to your “hardware bot”, do you mean like an LLM trained on hardware stuff?
Coming to the problem at hand, I went through another thread here on L1T forums and full credits to @Nefastor for explaining how the PCIE slots are configured on this mobo. If anyone is facing any issues similar to mine, I’d suggest going through the linked thread, I can’t explain it better than him. Basically, any weird configuration you want should go on the first three slots since they don’t have any redrivers and being closer to the CPU means the signal would not need any amplification. So I moved my two splitter cards to slot 2 and 3 and had 4 GPU’s coming out of it. Mind you I had to change them to Gen 3 speeds from BIOS or else the endless AER errors. I kept the bottom 4 slots for 3 GPU’s running at Gen 4 and one HBA card at Gen 3. I didn’t want to mess with the redriver settings in BIOS so I kept it simple but if anyone wanted to further split those lanes, then they would need to go start tweaking the BIOS settings for these redrivers in order to get it to work.
I did not need any special kernel parameters for Linux, as soon as I changed the ordering of the PCIE slots and adjusted the BIOS settings, Linux booted up fine so @Shadowbane 's hint about the PCIE configuration was correct. Windows must be pretty flexible if it was able to run the hardware without issues but Linux didn’t like it. As of now, this setup allows me to run 4x4090’s at Gen 4 and 4 at Gen 3 speeds + 24 SATA (on-board + U2 + HBA) drives and 1 NVMe drive.