Sorry for the late post, I just got registered. I had the same symptoms you've described, but it was my parking brake cable bracket rubbing on the driveshaft. I'd get a rubbing sound when I'd floor it and the 'stang would really squat; more often when the trunk and/or back seat were full. This situation is actually common on the 94-95's, not so sure about the 96+'s. It doesn't matter what kind of tranny, it's just a bad placement for the bracket. I'd be willing to bet you've got a nice shiny spot on your driveshaft, somewhere in the middle of it.
If this is what you've got, the only way to prevent it is to get an adjustable pinion snubber. That's what fixed it on mine. The pinion snubber is actually there to keep you from bottoming out your rear suspension. The adjustable pinion snubber's purpose is to bottom out on the snubber first, instead of on the chassis or the aforementioned bracket.
If you are actually talking about the yoke on the snubber, well that's kinda by design. Better to bottom out on the snubber than on something more delicate. You'd have to stiffen up the suspension to keep the rear end from dropping too far.
It adjusts to varying lengths, so you'll bottom out on the snubber (as intended) instead of the bracket rubbing on the driveshaft.
It's a three-bolt removal and installation. Jack up the rear end and place it in Jackstands. You can then reach the stock snubber by reaching around the rear axle. The adjustable snubber I got was too long; I had to cut it so it fit. If your car is stock height, you'll probably be fine.