Hmmmmm

The timing "spot on" is controlled by the computer....Moving the pump physically will not change things unless you go outside what the computer can adjust things....then the SES light will come on due to the timing being "out of range"

Injector POP PRESSURE can have a big effect on "Diesel Rattle" and depending on variations in the POP it can cause slight roughness in the idle as can other injector issues such as the spray pattern....A poor or odd spray can cause roughness too.

Were the injectors new or rebuilt ???