3" has got to be overkill, especially with a 2.5 neck down (or 2.25 can't recall).
Not to question your installation, but my mbrp droned so bad I was terrified it sounded like a fart cannon, inside cabin was very droney.
I checked and it was making contact slightly with the little protective plate thing they have you remove and replace. I moved it around a tad bit to free it up and my drone went down to almost none,and now I can hear the gurgly pops and noises it makes on decel and rev match instead of drone.
Again, not trying to question you. I'm no mechanic. There is a degree of drone compared to stock for sure, but if it's just unbelievably loud it might be touching the car somewhere.