I had this thud noise over small bumps. After you check all the shock bolts check the spare tire too.
If its neither of those, I found by rattling thud by banging on the frame and could hear the noise. It was the heat shield! That shield is bolted with 3 bolts. I dropped the spare tire, removed the heat shield, the reinstalled it with thick rubber washers between it and the frame... All 3 bolt locations. Thud nose is gone now!
1950 Willys CJ3A, all stock.
2010 WK, 3.7l, Rubicon wheels in Anthracite, K&N intake, Hypertech, 2.25" RRO lift, Bilstein 5100, Stillen brakes, 265/70-17 Hankook DynaPro ATM, Cupholder Ring LED's, Expanded Sheet Grill mod
UPCOMING MODS: Fastman TB, cargo LED's