Hey...
I've got an 02 Gt with the same problems and the dealer i dealt with put a new engine in and it did not cure the problem. From what i've learned Ford barely has anything beyond speculation to address this problem. Dealers across the country seem to be replacing the motors unnecessarily--and on the advice of Ford's own Tech hotline.
In my new motor i have some piston slap that is noticeable only in gear and driving at about 2000-2500 rpm.
There is also a pretty nasty sounding rattle (sounds like a marble on a countertop) at 3000 rpm or thereabouts.
Both of these noises are completely eliminated upon driving for 2-3 minutes. And both are noticeable only when cold (engine sets for more than 3 hours).
This is a huge deal with the 01-02 Gt, bullitt and Cobra cars.
The working hypothesis is that it is some piston vibration/piston slap.
www.bullittclub.com
www.stangnet.com
www.corral.net
No offense to Mustang Works but these sites other have a rather large Modular following with numerous complaints about this problem. I suggest doing a search for your problem on any or all of these websites.
My bottomline advice to you is not let your dealer put a new motor in it cause it ain't gonna fix the problem.
Also: ask the service manager if you and her/him can drive a new Gt off the lot to see if it makes the noise. I did this and drove two Gt's auto and manual and both did it (to the shop foreman and service managers surprise). If you do this, it will change their tune about putting a new motor in--in a second.