The fact you have two contribution codes is pretty telling right there.
Does it act like it's missing when you are driving? It's also possible they are old codes.

Clear the codes to see if they come back

You need to be able to read data live in order to start pinpointing problems

 

Sounds like you may be getting air in the fuel lines. You said you just recently changed fuel filters. Check and make sure they are tightened good and also check the o-rings in the caps and make sure they are both good (make sure they didn't get damaged during replacement). Also after you change the filters, make sure you cycle the key on for 30 seconds and then off atleast 3 times. This is to purge the air.

 

 

 

Did the engine dying issue begin after or before the fuel filter change?
Did you drain the water when you changed fuel filters?
Was the fuel or the filter very dirty or contain much water?
Have you checked the primary fuel filter cap o-ring to make sure it wasn't damaged? Same for the WIF (water in the fuel) drain plug ...... make sure the threads on the plug are good and the o-ring is good.

Typically a programmer is not the same as a scan tool when it comes to reading codes or pulling PCM information. Yours might be, but probably not. Tell us what you have ..........

As xcrsp440 suggested, ForScan will do the best job at scanning for codes. Just because you can get a few codes with a programmer or a scan tool doesn't mean that all the codes are being retrieved. Just like code readers, not all scan tools are equal. The Torque App and ForScan both do well at reading the PCM parameters from the sensor outputs (PIDs). They are phone apps and only require an ELM 327 adapter (bluetooth for the Torque Pro App and WiFi for the ForScan App). The ScangaugeII can give you PID information as well. It is clunky and a little expensive, but good for PIDs (not a good code reader though).

PIDS you need to retrieve and post first:
- FICM voltages (MPower, LPower, and VPower). The FICM is the computer that controls the fuel injection process. The FICM takes 12 volt Vehicle power and supplies it to the Logic board for Logic power and also steps up the voltage to 48 volts in the power board to send to the injectors (MPower).
- ICP pressure in PSI. ICP is "Injection Control Pressure". Your injectors are actuated with high pressure oil (you do not have a high pressure fuel pump).
- IPR % duty cycle. The IPR is the regulator (valve) that actuates to control the high pressure oil pressure at the desired point as determined by the PCM.

We need to see these values when cranking on a cold engine, when cranking on a hot engine, and at idle (hot and cold).

You also really should get a fuel pressure gauge. We did not even get a sensor for that from the factory, so you would need to add a sensor AND a gauge. Lots of threads on that. You need to read up on that - very important.

If you have low fuel pressure or air in your fuel, you will damage injectors and end up spending a LOT of money.

Check your fuel for bubbles (two person job). Remove the cap on the upper fuel filter. Remove all the fuel, Then turn the key on to fill the bowl. Look for bubbles as the bowl fills.