A brief update. Ive got my head gasket issues sorted well enough. Remilling the head didn't allow the copper gasket to work, I think I simply used up all the available compression of the copper (it measures thinner now). A composite gasket with fire ring was made as planned and is working so far with no leaks.
On to the next problem, fuel. I made a new, heavier spring for the injector, which prevents compression blowing back into the fuel lines quite nicely. However, with the stronger spring tension the injector no longer sprays fuel. Cue half a day spent chasing leaks... The initial culprit was the injector needle seal, which seems to have been damaged. Replacing that led to finding leaks in crush washers, the cone connector to the injector, etc. all easily fixed.
Finally, I got to the plunger and barrel themselves. Bad news there, the fit clearly isn't good enough. I noticed fuel was leaking below the pump, and actually ended up submerging it in kerosene and applying compressed air (using a syringe and tube connected to the fuel inlet). Bubbles leaked from the back of the barrel with only modest pressure. Seems I need a new plunger and or barrel
Now normally I'd just say oh well and get on with it. However, my partner has just recently got a job offer in Germany, and so it's likely we will be away from my shop for two years. I'd like to see the engine run under its own power before we go, so I'm weighing up whether I should convert it to a petrol engine and get some running done to validate the other parts of the design, then revive the diesel side of the project when I get back.