Do you have an aftermarket shifter (Steeda Tri-ax, MGW, etc...)? If so, remove the shift boot and see if the handle to base bolts are still tight.
Do you have an aftermarket shift knob? I had the Mach 1 knob and it rattled like crazy so I changed it out for a different knob
Do you have aftermarket exhaust? The headliner rattled if it was below 60* when I had my o/r H-pipe d/t the resonant frequency...
Dude it could be a million things, we need more details on where the sound is coming from and what it sounds like