Hats off to you darbuck, you sure are chasing a lotta gremlins with this beast!
I don't know much about Pug/Cit diesels yet but have chased the injector problems myself - specifically cylinder balance issues.
Fairly certain you have at least one tired/worn out injector based on the deviations in injection timing.
The ECU detects that one or more injectors are not firing as fast as it/they should, and it then tries to either speed up/slow down injection timing and/or quantity to compensate and level out cylinder contribution.
Most diesels use both the crank & camshaft sensors to detect even slight variations in RPM and since ECU knows which cylinder is firing when, it will try to level compensate.
Some diesels use knock sensors too, but I don't know if yours does.
One fairly easy thing you can try is a leakback test of injectors, just to confirm which injector might be giving you grief.
Still it won't tell you if the solenoid is worn out. ECU could very well just be retarding/accelerating timing but injectors will still use the same fuel overall.
Sorry if you already tested leakback and know the problem, I was too lazy to read every page
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