I can't see its a timing issue if the engine runs properly when the misfiring has ceased. By this I mean both camshaft and injection pump must be timed properly for this to happen.
You have the Roto-diesel pump. the cable from the waxstat device i referred to passes along the front of the pump (nearest the radiator) and its quite easy to see if its working. Its function is to operate an electrical switch which in turn advances the timing for cold start purposes. This is in fact dependant on the engine hot idle speed to some extent.
I had one fail on my TD BX and it had a very slow cold idle and would tend to hunt.
If you take the rocker cover off you can only inspect the valves and of course check the clearances. You would find out if one or more was tight and it is possible to re-shim with the head in position. The other possibility is small cracks in the head which seal as soon as the combustion chamber gets hot.
Have a look at the waxstat cable - which should close the switch when cold. If it hasn't, close it manually and see what happens. (switch may be inside a small rubber bellows).
jeremy
Smokey Joe
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