My 98 Cobra had a sound that was slightly like a leaf in the heater fan that has gone down through the defroster vent. After several years of it making this sound, (when the fan was on high) it finally burped out a piece of foam rubber insulation. It spit out small chunks for quite some time. Last year, the 99 F250 did the same thing and it still spits out little crumbs of foam now and then.
It is a thin, lightweight foam rubber material that I believe is used to prevent air leaks and rattles in the system. I think it overlaps in there somewhere where it shouldn't and flaps around when the air is moving making a rattling kind of sound.
I never tore it apart to find it, too much of a nightmare.
I never got the pleasure of the one under the shift boot.
KJK