I have a tri-y header and 2.5" tube with a 2.5" magnaflow 18" big body muffler, and it's loud and annoying!  With my previous setup, I was all 2.5" and stuck in an extra 2.25" glasspack to quiet it down for deer season and lost bottom end.  Jetting did not bring it back, the extra restriction seemed to remove my low end snappiness and response.  I'll never neck down small again if running a header, but this shouldn't be the case with the stock manifold.