I've got the same rattle! It's beginning to get louder and louder.

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2003 4Runner SR5 V6 4x2 - Pacific Blue Metallic/Taupe Leather
Factory Installed Options: AP-Appearance Package, DR-Roof Rack, CF-Carpet Mats, SR-Moonroof.
Added: AW-17" 5-spoke Alloys on Michelin Cross Terrains, NJ-Homelink, RL-Daytime Running Lights, G0-OEM Stainless Door Sills, HP-OEM Hood Protector, E5-Valor Exhaust Tip, GN-Cargo Net, 3Z-First Aid Kit, 7R-Emergency Assistance Kit, Bartlett Avalon Fawn Leather Interior, All-Weather Mats, Spare set of OEM carpet mats, Leather-wrapped shift knob, Scion T1805 6-Disc CD Changer, Driver's Assist Handle, Wide-angle 5-LED super-white map and door lights, Xenon super-white dome lights, Silverstar ULTRA Low beams, Silverstar fog lights.
In Progress: Leather-Wrapped Steering Wheel with Mounted Audio Controls.