Well I messed with the timing a bit more, installed new injector seals and started running it up and down our driveway (steep hill). It gradually got good enough that it would idle but still bumped up and down. Really strange how it slowly got better. But at least it will pull under full load without smoke or missing anymore.

The power is back and the turbo will spool again, but as soon as it drops to idle it starts with the rich diesel stink, blue/grey smoke and poor idle quality.

After messing around in the lot with it for a while it was good enough to drive on the road again. Once on the road it was very nice. Great power, no visible smoke but idleing at stops it would still bump and misfire a little. I fed it some Dex3 tranny fluid and drove it some more and a little harder, its getting better but still not quite there.

Sometimes it will purr like a kitten smoother than I've ever seen before but then it will start to shake intermittently again. Since its drivable again, I'll drive it to the diesel shop that did the work on the pump to see if we can make some sense of what is going on.

Earlier I did try to run the injector pump directly out of an oil jug full of fuel to rule out any potential faults in the fuel system of the truck. The results were exactly the same, so I think the fuel system is good. The filter has only a couple hundred miles on it.