Very slightly Loosen off the two bolts that hold the door latch striker plate (shiny bar thing in the door shut ) . Don’t loosen too much so that it moves by hand, just crack them loose a little then close the door and open it a couple of times. This should locate the plate to the correct position. I’ve used this method many times and always solved any sticky clunky door closing/opening. Oh just in case you undo the bolts too far and the catch plate drops out of position make sure you first surround it with masking tape and draw some locating marks so you can always return it to its original position should you need too.
As the mk1 Nismo was never released here they are pretty hard to come by but well worth the hassle and cost. I’m not really a fan of dark wheels neither but for some reason they seem to suit the z
Could be coincidence that this is happening after the tune. Could be that the maf sensor needs cleaning, dodgy plug or coil pack, o2 sensor,water temp sensor, dirty throttle body?