Bad knocking under feet

I bought a Duster with a Ford 9" in it. WTF are people thinking. Anyway ...

I had a bad noise in mine after I swapped it for an 8-3/4. The first time I took it out I brought it straight back barely moving because I was convinced it was going to puke the driveshaft out of it. It took a little while to figure it out, but eventually I noticed the witness mark from where the driveshaft was hitting the exhaust. The exhaust was built too close to the driveshaft, and the different offsets between Ford and Mopar rear ends caused the driveshaft to hit the exhaust after I switched to the 8-3/4. It could be something similar in the OP's car.
Very interesting. Did yours have stock manifolds? Mine has completely stock exhaust, so what you said sure makes a lot of sense.