NRF9160DK no AT commands and NFC has modem firmware button greyed out

Question

After getting my nRF9160DK activated and showing up in the NRFCloud it would just sit there blinking led3. 
 I deleted the device from the cloud and tried to update modem firmware to the latest 1.1.0 version. 
 I have NFC 3.3.0 with all the correct plugins and the latest NRFUtils and JLink etc.. The programmer plugin can wipe the device and write any of the .hex files from the download section but the reset and the modem firmware buttons are not enabled. 
 
 When I try the LTE link monitor it shows that the device has three serial ports none of which work... 
 
 The first two allow connection but do not accept any AT commands and entering any command generates an error... 
 
 I think I need to re flash the modem and add a certificate for it to see the cloud site again. 
 Although I purchased this device recently it seems to be an older version i.e. is only has an imei number but no password on the sticker. 
 How can I get this back to factory with the latest modem firmware?

GazzaD · Answer

Using the 9160DK's jlink/Debug out I was able to loop the programmer back onto the board on the P3 (nrf91 Debug) 
 
 This allowed me to access the 9160 from NRF Connect and update its modem firmware and the Asset Tracker. 
 I repeated the process using the P11(nRF52 Debug in) and programmed the board FW hex file. 
 After reset I could connect via the USB to the LTE Link Monitor and using the second listed port access the modem via AT commands. It connected to LTE but was reseting repeatedly. 
 Next I logged into NRFCloud and requested a new cert using the boards imei Number and its Mac/HWID found on the sticker. This downloaded a JSON file that could then be used to update the modems certificates. 
 The board was powered off and the sim removed. Opened the LTE Link Monitor powered on the 9160DK and could see it boot in the console. Next step was to use the AT commands to make sure it was working and to shut off the cell modem with AT+CFUN=4. 
 Updated the certificate and reset - 60 sec later it was connected !! 
 After that it was a simple matter of adding the device to the NRFCloud and making sure that it was added using the imei and MAC/HWID used to make the certificate. 
 I now have a fully updated nRF9160DK that is attached to the nRFCloud. 
 Remaining questions... 
 According to the documentation all of this should be able to be achieved using just the USB connection. NRF Connect still only allows the erasing and programming of the nRF52 even though it sees all three usb ports... 
 
 When this device is selected it reports ... 
 
 It's not seeing a NRF9160 and hence the modem firmware update is greyed out. 
 I have been using the latest board Firmware in the 52840 and the latest modem firmware(1.1.0) and asset tracker in the 9160. 
 The nRF9160DK is Rev 0.9.0 and NRF Connect is version 3.3.0. 
 At this point the only way I can access the 9160 is to use the loop method from above.