Please make sure you could boot up w/o NVMe drive first.
Then, you could refer to the following instruction to flash into NVMe drive for rootfs. Flashing to an NVMe Drive
Do you get the BSP package from your vendor?
What’s the Jetpack version in use?
I don’t if there are reset/recovery buttons on your custom board.
Just use jumper to short recovery pin and GND, and give it the power, then it should enter force recovery mode.
You could use lsusb on your host PC to make sure the status.