My situation is kinda similar to yours. I also had no service and got an Unknown baseband message in Settings when I went from stock rooted MK2 (with stock MK2 kernel and MF9 bootloader) to the new NAE ROM and NAE baseband.
I suspect that NAE requires a Knox bootloader for service to work.
Anyhow, to go back to a fully functional MK2 state, here's what I did:
1. Restored my MK2 Nandroid using Philz's recovery.
2. Booted directly into Download mode from Philz and flashed back the MK2 modem with Odin 3.07.
3. Rebooted phone and everything fully works again.
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