Use caution on fordparts.com for determining part numbers. The GT500 alternator is KR3Z-10346-A and the pulley is not sold separately.
The part numbers listed above for the 5.2 are referring to the GT350 5.2
One other thing to consider, is to the outside world the Roush and Shelby American built cars VIN will show it as the Mustang GT (P8C I think) they are built on. This could be an issue from an insurance and/or financing perspective. When Ford builds the Shelby models they have VIN that reflects...
8592B in illustration (post#4) above = KR3Z 8592 A
8592A in illustration (post#4) above = KR3Z 8592 B
There is no direct correlation with the letters on base/callouts in the catalog illustrations with the service part number. Sometimes they match sometimes they don't.
When they sold the fleet the cars were 16s maybe some 17s, IIRC they never offered any of the 19 up GT350 cars for sale. And yes most if not all the ones offered had engine replacements (sometimes more than one) and some had transmissions as well. There was a list posted somewhere with all the...
I made a similar recommendation earlier. On some level the the dealership is almost punting on figuring out the root cause and wanting to replace the transmission might not be helping the OP with a more expensive bill that will attract attention.