The trunk liner may be the rattle problem
I recently posted on AFM about a rear rattle coming from the passenfer rear side. I would check the inside trunk liner. On either side of the deck lid, there is one panel clip (one on each side). Each side has a clip that slips over a stud. The liner secures to the clip with a plastic plug insert. The problem is that these clips (used predominately throughout the vehicle) fit really loose on the studs and will rattle even when the liner is secured with the plugs.
How to resolve:
I cut a 2" long piece of rubber tape (one for each side) and folded it over the fender stub. Take a utility knife and cut an 'X' into the hole to allow for the plug insert. Reattach the clips squarly over the studs; they should be nice and tight. Reattach the liner with the plugs and you should hear any more rattles.
Hopefully, this will resolve your rattle. Otherwise, you should check:
- spare tire - make sure its tight
- lock latch trim cover - edges of cover make rub on underside of deck lid. I attached the felt side of a velcro strip by folding over the edge of the cover.
Good luck!
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2005 Mustang GT, manual, Windveil Blue, Premium Pkg., Shaker 500 System, Ford Alarm System. Sequential turn-signals, plenum cover. rear-lowering springs, hood lift kit, and other minor dress-up items. Prev. owned: '65 Coupe, '84 GT, & '86 LX w/ 5.0.