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That black smoke IS incompletely burned diesel FUEL. This is a result of "overfueling" be it from insufficient turbo boost, poor state of tune, etc. So, essentially, it is hydrocarbons.
That will not go away no matter what happens ie: low sulphur fuel.
Another thing is NOx. This happens when ... do I need to get into chemistry? Long story short, it is a result of high compression ratios and high combustion temperatures, both inherent "qualities" of diesel engines.
Something to think about: These are the only two things that a diesel engine is a gross emittor of. Gas engines pollute 4 gasses. They are HCs, CO, CO2, NOx.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.