Here is my opinion from experience
My car had the clunkityclank from the day I got it when it was completely stock. When I upgraded the suspension-UCA's, LCA's, springs, add on adj. swaybar, Illumina shocks (all this on the rear)-it got worse. I double and triple checked every bolt and nut and that everything was on correctly. It was. So I added an aluminum drive shaft. It got even worse.
Here is my theory. The Mustang is designed with slack in the drivetrain. When you tighten up things around the slack, this lessons the ability of the suspension to absorb some of that slack so you hear it even more. Pretty crappy, huh? IF I am correct on this theory then the only thing I can do is when I have the rearend rebuilt, have them set the tolerances a little tighter than stock. I know this can be done safely. That may alleviate some of it but I think some will always be there. I believe it is in the design of the upper and lower control arms. When you press the gas and this puts force on the drivetrain it causes the differential to buck up and down at the front where the driveshaft connects to it. OR should I say rock up and down. The pinion angle changes. If you stiffen up the suspension, it can't absorb this rocking like it used to. IF you stiffen the driveshaft....same result....less absortion.
I have to make sure my pinion angle is exact on. I have not done this yet. I know it is within range but have not been able to check it for exact degree yet. Been lazy. This may help a little. I have new engine a transmission mounts to go in. Getting around to it sooner or later. May help some. Have to wait and see.
What I find hilarious about it Is that when I am hammering the piss out of my pony she is rock solid and doesn't make a sound. BUT if I am cruising down the interstate and let off the gas to slow down and then press the gas again, it sounds like the rearend is falling off. If I "blip" the gas peddle....Holy Cow it is like the rearend FELL OFF. Too funny.
I'm tired of typing now.............Ken