I've made this interesting discovery in my car, that has been the same in two other 'Stangs. I had a bad clunk, and could never figure it out. I put in a new clutch, flywheel, throwout bearing, pilot bearing, pressure plate, shift fork and ball, u-joints, all new bearings in the rear end, and a perfect lash adjustment, and still had a clunk on shifting. Turned out to be the upper control arm bushing, where it mounts to the body. The inner steel piece that the bolt went through was too wide, and when the axle would move, it would clunk up there. I had a friend kick my rear tire from the back while I was under the car, and I saw the thing move. I'd check your UCA bushings, because this has been the same on two other Mustangs I have worked on.