Two of my birds have made strange clunking noises, both of them were traced down to the exhaust. One of them was too close to the left rear suspension and was rubbing where the A Arm bolts too, made strange clunking sounds. The other one was laying on the brace that runs right in front of the pumpkin. It would only clunk when I took off, as then engine and trans would torque it up off the brace and then lay it back down.
To put it short, i would check the exhaust also. A used pumpkin with good gears is fairly cheap and not hard to install if that turns out to be your problem. Good luck.