The Hilux uses a typical ladder chassis with plenty of room in the engine bay so engine options really aren't a problem. The rattles are pretty normal, especially when cold so I wouldn't normally consider them a part of your problem. By the sounds of it something is causing it to run rich. My theory would be that you have a heavily clogged intake. Carbon buildup in the Hilux intake is a common issue, some get it worse than others for no apparent reason, and sometimes the carbon can restrict the intake quite badly. With so much restriction in the intake, the engine would tend to run rich (hence the black smoke) and as the revs increase there wouldn't be enough airflow that it might trigger an error code/engine cut that some people experience when blocking the EGR valve (ironically, the biggest cause of carbon buildup within the intake). Try removing the top half of the intake (intercooler, throttle body right down to the EGR valve above the lower intake manifold) and inspect it, cleaning it with throttle body cleaner if necessary.