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i did the same exact thing. i have an Apex N1 muffler and i got 2 1/4" piping and i got the resonator taken out. i think its better with the resonator out.
Its personal preference really. I prefer a quiet near stock sounding exhaust. If you want a really loud exhaust that you can annoy people with, go w/o the resonator.
Originally I had a straight 2.25 pipe and after a while it got old. It's just WAY too loud. I had them put in a foot long resonator and it sounds very very clean now. JMO