Any low-frequency thump, thud, or clunk, especially at acceleration, is typically traced back to bad mounts.  Check both the engine and transmission mounts to see if they are bad.  Loose or broken engine and / or transmission mounts can cause these types of noises.
FC3S Pro:  Mods, Transmission Fluid
FC3S Pro:  Problems, Components - Transmission Mounts
FC3S Pro:  Problems, Components - Engine Mounts

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