Retarded injection pump timing could cause excess smoke as engine cannot really sustain good combustion when cold. Smoke should be blacker rather than blue though. Just to check it is not hard. You need an old injector line to make a drip tester basically. Only if it is way out go further. I believe it should be done on any new aquisition including a chain stretch test. The pump cannot move itself. If injection pump timing is way out it has to be excess chain stretch usually. The primary flaw in what I suggest is that a retarded timing usually causes the engine to be a little harder starting than the same engine timed right. Your statement that it starts right up is not particularily condusive to checking it. On the otherhand your current misery is not going to go away itself unless you have a load of bad fuel so why not do a quick check? You would not want to do a lot of things and eventually end up back at the initial pump timing. Of course the above standard size bubble in the primary fuel filter means you could check for air getting in as well I guess. You could also look very carefully to see if small air bubbles are working their way through the primary fuel filter as well. Although an air leak could be past that point as well. Your description of events has been noted reciently with a badf secondary fuel filter as well it seems. You have changed that already. Although I am not sure how it actually causes the effect. . It could also be a combination of a couple of deficiencys.