Looks to me that you have the correct parts. Your 8.8 has the factory stock flange on it not the Cobra flange. The Shaftmasters drive shaft looks like it has the correct flange on it to fit the stock 8.8 flange. It may be a snug fit but it should go in. You may need to use the bolts to pull it in. It will use 6 bolts where the Cobra flange would only have four like you original V6 driveshaft. If the kit did not come with the six bolts you will need to pick them up from Ford.
2006 V6 PP
Explorer Express - X-Charger SuperX TVS (Prototype)
Tremec TR6060 6-Speed Manual Transmission