COnsidering the final corrected parts for the T-3650 just became available on July 20th, i doubt he has a good fix in it. Most of the early fixes end up failing in the long run.
Not all '04s have the final revision transmission. SO early models may also have the grind/clunk. I've seen '04's with 200 miles on them clunk right from the beginning. Even the later ones don't have the same parts that became available in the TSB that came out.
Oh, most importantly, you can't install this transmission in a 5.0. The t-3650 has an integrated bellhousing that's part of the trans. This tranny was designed with Ford's modular motor in mind and it's only used on the Mustang GT, Mach 1 and the Ford Falcon and a few other aussie cars with 4.6's and 5.4's. The bellhousing is machined for the mod motor's bolt pattern and there are no adapters.
So without getting into what a load the T-3650 is (even though it's stronger than the base 3550 rated at 360 ft-lbs) you can't even run it on your 5.0.
I'm taking my '03 GT to have the TSB performed on my trans. The 1-2 clunk gets annoying on those cold rainy mornings.