Was testing only from serial ports of the PCIe serial card (in the case of the built-in serial port testing)? I just want to verify J17 was not involved since this is linked to the camera module.
From the 16550 serial port card failure, is there any kind of log or OOPS message you can post? It would help to see how much of this error cross sections with the onboard serial port error.
EDIT: I just went back through some of the thread, and have another observation. This is a custom board, so I assume there is no camera module attached. However, there would still be firmware or other setup to link what was J17 to the camera module unless you’ve modified this. Are you sure there are no firmware or other content which might interfere with using the serial UARTs for custom purposes?
If you want to browse a dtb file from “/boot”, dtc is built in kernel source at “scripts/dtc/dtc”, or else can also be installed on the host. This would reverse a dtb file and provide a human readable dts (though any original source code comments or naming would not be present):
dtc -I dtb -O dts -o /tmp/extracted.dts /boot/the_firmware_in_extlinux.dtb