I was looking at a 1999 Cobra and whenever I would accelerate there would be a knocking/banging in the rear end. This has me thinking that the pinion and planetary gears are worn within the diff. Are there any other reasons I could be hearing this sound?
Usually if your gears/bearings are worn enough to clunk you will get moaning and or whining sounds(if your exhaust isn't to loud to hear it), especially on the freeway with the windows up and the sounds off. Jack it up and jack stand it and climb underneath and check it out, its not rocket science, should be easily discernible.
My 03 does that in traffic between decel and Accel. It's just the play between the contact point on were the ring and pinion gears mesh. If you start hearing a loud/loudish whine/roaring noise that increases with vehicle speed then you may wanna look into a diff rebuild. My old gt started doing that. Was noticable at 70+