Why does my car makes noise from the engine and cut speed normally makes it at 100km/hr so it reduces the bad sound whenever I leave the accelerator pedal

I have a diesel 1kd prado that show ''fuel filter maintainance requiered'' on the dash board. Have since changed the diesel filter on the lift pump but nothing. It even started going off as i drive so… 

Some engine chek comes and car shake while gear shift

There's a noise on my engine

Engine noise and road noise are coming inside cabin

When I first start my car in the morning, some noise coming out from engine