Can it read scan data??
When it acts up you need to monitor your Injector Control Pressure ( ICP ) needs to be at least 500 psi at ilde or the Injector Driver Module won't fire the injectors.
You also need to see the Injector Pressure Regulator %
Default for unplugged is 750 psi for the ICP
Also check the nut on the IPR and make sure it is tight, if it is loose it will allow the electromagnet on the reguator to move causing pressure spikes or dips.
And since the PowerStoke does not fall under OBD II, there are most likely more codes stored that it can't read.
Example: I was working on a 2000 Dodge with a Cummins, on my laptop in Generic OBD II mode, I pulled two codes, by the using the VIN enhanced version I pulled 7 codes.
Also don't forget, these are famous for Cam Sensor failures, doesn't always leave a code. I would pickup a spare one anyways, they are down to about $20
Goodluck