I wrote Ford and they confirmed your suspicions: The 05 V6 only comes with 6.7 Manly Points, or MPs, while the 05 GT has a whopping 8.3 MPs. It seems you are on to something! They weren't keeping official MPs on the 04, but an anonymous souce told me that an 04 GT was giving off 8.8 MPs at the flywheel.
They also said that they included more "dash crawl" room in the 2006 V6s, and plan to eventually let V6 owners drive from under the dash with an impressive array of mirrors and sensors. Thanks for the valuable information! Keep us posted, won't you?