with the bigger injectors it throws the timing off. adjust to around 16.5 deg. and the pop and white smoke should get better.

When I advanced the timing on mine (16.5) it is harder starting in the cold. The idle is smoother and gained about 1-2 mpg. Nothing else.
Not sure about rough running, I never move the truck until it is warmed up.

Advancing the timing will make it harder to start, ever hear a pulling truck with 30+ deg of timing try to start? It is also not "typical old diesel" or "sounds about right" If it has been plugged in all night it should start with minimal cranking and run pretty decent, it won't be happy but it should fire if the rest of the system is in good order. I will give a vote for losing prime as well.

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Bigger injectors have nothing to do with timing, if the timing hasn't been messed with. All they do is deliver more fuel per cycle.

if the popping pressure is different it will change the dynamic timing

If the POP pressure was that different, it would act like that all the time hot or cold. If they are new(er) injectors, especially from a reputable dealer, I believe this would not be the problem. If they are older or bought used, They should be tested anyway to make sure they are within spec. This however does not sound like the problem seeing as how it "goes away" when warm.

what do you do if the pump is loosing prime? i think that that is what mine is doing cause after mine sitts a while i have use the pedal a little bit to start it:dang:

Replace worn or cracked lines. 99% of the time it is the rubber lines but every now and then someone hits steel line when they are working on it and "breaks the seal". Make sure you look at ALL the rubber lines, right from tank to pump. Although rare as well, make sure the seal on the lift pump is still good as well.