jeff11

ECU Talk will never work with OBD2 adapter sorry incompatible protocols! You will need to use Consult II interface/adapter those cables are available from its website.
I'd be lost without it.
Code 0406 :
An excessively high voltage from the mass air flow sensor is
sent to ECM when engine is running.
If there is NOT 0102 code present it is likely that MAF sensor is not faulty and actually measuring high air flow.
Possible causes are:
However above doesn't take in to account that you have:
Blocked EGR, fitted 3" exhaust and left stock controller in the place. What that does is causing it to overboost and triggering safety "limp" mode in certain RPM range.
This is well known to all of us who mod this POS.
if you get 18 psi out of yours and that's why you are getting that code!
 
Code 1003
probably cause it is either disconnected or other way electrically disabled, normally we leave it connected electrically and block the port with metal shim so ECU is none the wiser as it doesn't actually measure the EGR flow like on much later vehicles it just guesses so it is dumb and to our advantage.
 
Code 0407
If you see bare wires then yes not good, I will attach some info on checking these codes, bare with me

Are any of these codes active?
You really need to see what ECU is doing and its sensors.
ECU Talk software with its Nissan Consult II adapter cable can read the sensors in real time so you could use it to pinpoint cases.
Pump harness is reasonably accessible however I'd not call it easy. 
Regards

G'day,
Disclaimer: I don't know wiring setup on Navara.
On Patrol red wire comes out of pin 2 on pump side (9 pin connector) and is for CAN High (CAN-H)

 
leading in to the Nissan style plug 6 pins (near  intake manifold)  pin 2 on the Nissan side becomes red with black tracers wire. Essentially that short harness is just patch lead to adapt to Nissan style plugs.
Regards