Changing exhaust systems shouldn't effect your warranty, it will only void the warranty on the exhaust system, which you have taken off and aren't using anyhow. The aftermarket stuff you have added wouldn't be covered by Ford naturally. If you had the exhaust system put on at a muffler shop go there and have them check things out and see if any of that could cause your noise. If not you shouldn't have to remove it to go to Ford. Just my thoughts.
Rick Kilpatrick, AAS Automotive Systems Tech, Alamance Community College, Class of 99. 06 5 speed manual Mustang with Pony pkg : GT Mac Mufflers, true duals with one custom pipe. 2.5" system. GT bumper cover, all installed March 7&8 2006. AFE Stage 1 CAI, Motoblue Underdrive pulley, GT aluminum shifter knob, honeycomb rear blackout panel,and dash kit installed. Roush hood scoop and side window louvers installed. SS taillight trim has been installed, new alum. GT steering wheel installed.