1. Bad Rear Shocks: Worn or damaged rear shocks can cause the vehicle to bounce excessively, resulting in a thud sound when the shock absorbers fail to properly dampen the impact.
2. Broken or Worn Leaf Springs: Leaf springs, which support the rear of the vehicle, can become weak or broken, causing the axle to hit the frame or other components, resulting in a loud banging noise.
3. Loose or Damaged Sway Bar Links: Sway bar links help control body roll and stability. Loose or damaged sway bar links can cause a thudding sound when the sway bar is unable to effectively stabilize the vehicle.
4. Damaged Trailing Arms: Trailing arms are responsible for locating and supporting the rear axle. Damaged trailing arms or their bushings can cause the axle to shift and produce a thudding sound when encountering uneven surfaces.
5. Loose or Damaged Shock Mounts: If the shock mounts, which connect the shocks to the vehicle's frame, become loose or damaged, the shocks may move excessively, causing a thudding noise.
6. Rear Differential Issues: Malfunctioning rear differential, worn gears, or damaged differential mounts can create a loud thudding noise when the vehicle is in motion.
7. Damaged Spare Tire Mount: Although you mentioned removing the spare tire, check the spare tire mount and the area around it to make sure nothing is loose or damaged, which could cause a loud thud when the vehicle encounters bumps or rough roads.
Identifying the exact source of the thud sound may require an inspection and diagnosis by a qualified mechanic. If the problem persists or worsens, it's recommended to have it checked and addressed as soon as possible to avoid further damage or potential safety hazards.