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Old post but in case someone else has the same question, On a mustang, nothing.
There is only a difference in the 09+ 5r55s for the mustang where they updated some of the fluid paths of the trans and thus the valve body. Other than that, 05-08 mustang 5r55s trans are interchangeable.
As slow as this forum moves a 6 month old post is not old.
Hollander interchange manuals the ones that were a foot thick were a good source for that information. But I thinks they went the way of the Dow Dow bird.