QSX15 hard start/extended crank times w/black smoke

[Running rough]

running stock (designed for EGR gas) timing without the egr, and or overfueling will cause severe valve seat wear, you have unsafe programming and i would fix that and replace head with new not reman before the valves drop and grenade your engine, if it was my engine i would cut counterbores and shim a and raise liner heights to .014, of course this calls for complete overhaul and reprogramming, but its the only way to be reliable going forward, my 2 cents