Hi, welcome to JustAnswer!. This is Ed.
You've covered this pretty well, but I do have a few concerns and we'll press on from there if needed.
To start with, let's check spark strength at any of the plug wire ends. You've got entirely new secondary ignition now (except plugs and coil) and putting the cap and rotor seemed to have a good effect for a short while. If spark is weak from the coil, it might explain why you're being made to suffer.
Next would be the engine coolant temp (ECT) sensor, located down between the alternator and compressor. They sometimes leak internally, creating a mound of coolant kak around the connector and at that point they're not very accurate. If your sensor has any signs of discharge buildup or a connector that doesn't sit straight up, it might mean that the sensor is lying its butt off at times. The actual ECT sensor is the 2-wire unit, don't be fooled by the single-wire sensor as that one is used just for the gauge.
And then there's the actual fuel in the tank. If the customer happened to pump a contaminated batch just before this problem began, you might be seeing the effects of water as it migrates to the injector rail. Taking a fuel sample from the pressure test port in a clear plastic bottle will tell you if it's anything but the clear, pilsner-colored stuff that you want. Also note whether the fuel that gets on your fingers evaporates completely within 60 seconds... diesel fuel will leave a residue behind.
These are just a few thoughts to get us started. I expect that spark will be the problem -- you should see at least 3/4" at the plug wire ends -- but with your help and a little patience, I'm sure we'll crack the case.
The 5 degrees of cam-crank offset is plenty-good by the way. I'm glad your scanner can check that.