Do you have the Access Cab or lift blocks for the rear of the truck? that might be some of the problem. i didn't have to install those on the double cab.
Hey Flavtfan, I have the Truxx kit also, And im always hear little thump noises like when drive on unevn dirt road or backing out of my drive way where thers a small dip. Sounds like its coming from the rear. Have you ever had the same sounds.