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Sounds to me like something got down into the blower, I had a '64 Corvair that I had to park outdoors and was always getting leaves and small twigs down into the blower...
Of the three Mustangs we've had in my house, a 94, 97, and 99 all with well over 30k miles(mine has 115k), the countless people I've known with Mustangs, and in my year working at a Ford dealership as a technician I've never heard of this thud in my life.