I own a 2001 Cobra and previously owned a '99. Actually I think I was the first owner to post a message about the vibration and get the ball rolling toward Ford's finally recognizing the problem. You might be too late, but in '99 Ford issued a TSB where they replaced the transmission, driveshaft and differential with matched and balanced units. It helped with the vibe, but didn't eliminate it. Because of the balance problem and the low horsepower, Ford gave all of us '99 SVT owners a free leather jacket (wow). The 2001's still had the problem, especially if you put in a taller gear. Of course, you might have some other balance problem, but I assume you've checked the obvious.
The problem is that pinion runnout and driveshaft balance tolerances are OK for a live axle, but they are too large for an IRS system which tends to transmit vibration to the body. The easiest fix is to use driveshaft balance to offset the pinion runnout. That's essentially what Ford did with the recall. You might want to get your driveshaft balanced before you try this, but I didn't find that necessary to eliminate 95% of the vibe.
Buy a cheap dial indicator from Harbor Freight, set it up securely under the diff and find the point of maximum axial (vertical) runnout on the pinion flange. Then put 2 hose clamps around the driveshaft with the screws positioned opposite eachother. It doesn't take a lot of weight to dial out the vibe, so instead of starting with the screws up around 95 and 265 degrees, start at something like 135 and 225 degrees. You need to do a bunch of road testing, but you'll rotate the clamps away from the point of max runnout (keeping the screws opposite eachother) until you decrease the vibration to an acceptable point. Adjust the clamps, road test, repeat....
We worked over this issue for a long time back in '99-'01 before we finally settled on this fix.
This url will take you to a good explanation of the problem and another approach at fixing it.
http://www.lx.net/jlynch/fieldbalance_r1.html
Good luck.
Jeff