- Try using a different USB flash drive, preferably 32 GB or larger.
- Format the USB drive using FAT32.
- Open Windows' built-in Recovery Drive utility and create a recovery drive. Make sure you uncheck Back up system files to the recovery drive.
- Download and extract the Surface recovery ZIP file.
- Copy all the extracted files and folders directly to the USB drive. Do not copy the ZIP file itself.
- Safely eject the USB drive and try booting your Surface from it again.
You can follow Microsoft's instructions here:
Creating and using a USB recovery drive for Surface
Also, check the UEFI settings:
Shut down your Surface Pro 4.
Press and hold the Volume Up button, then press the Power button.
Once inside UEFI, make sure USB boot is enabled.
Check the boot order and Secure Boot settings.
Save the changes and restart.
To boot from the USB drive, hold Volume Down while pressing the Power button.
One more thing worth checking: Since you have replaced the motherboard, make sure the replacement board is from the same Surface Pro 4 configuration as the original.
Although you downloaded the recovery image using the serial number displayed in UEFI, the replacement motherboard may have a different hardware configuration or firmware history, which could be relevant to the issue.