I have the same sort of thing with my 2002 PD150 - not major rattles, but vibrations from the dash. Impacted when pullig from low revs.
I have replaced standard head unit also, think that is cause. I also think that the Alpine V12 amp and MTX bandpass sub in the boot have loosened the trim within the car, after being pounded for 18 months.
Haven't bothered to give the dealer a hard time, as I know exactly what they'll say - you shouldn't have installed that stereo, so I do the same as Key - turn up that stereo!