Strange Noises (tranny?, transfer?)

[Kurt14]

Ok So, I'm in the process of saving up and purchasing Under-Drive Pulleys and a Custom live tune from PHP. But, before I get any of that done I am trying to diagnose the noise issue I am having. I have recently replaced the U-joints, checked the rear differential, and replacing fluids with synthetic RP. The noise is a thump-thump-thump-thump-thump you can hear it only and best at low speeds say 28 and under, out of the throttle when coasting, noise almost disappears when put into neutral. I am in the process of becoming an automotive tech but am having issues diagnosing this issue and it's really worrying me. I have taken it to the local Vernie Jones Ford dealership but absolutely will not return there. They always give me the run around and don't want my business. Absolutely drives me crazy. I'm thinking I caused this issue from when I first got the programmer I turned the shift pressure up high. Anyone deal with this or have any ideas?