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For '09 the 2V (16V VIN CODE W) came with the 4 speed transmission the 3V (24V VIN CODE 8) came with the 6 speed transmission
I (still) have the '09 XL that I bought new, I specifically wanted the 4.6l 3V, It was on the lot, they had 4,XL's:
1 - 4.6l 2v, 2 -4.6l 3V's & 1 5.4l 3V................. I bought one of the 4..6l 3V's that had the color I liked best (Royal Red).
IMO the 4.6l 3V was the best combination for me, better MPG, HP and torque for towing (aka the life of an XL truck)
I think the 6 speed transmission has the lions share of the better MPG.
The trade off is the 4.6l 2V is IRON clad reliable,
Both the 4.6l 3V and 5.4l 3V's need to use 5W30 oil vice Fords recommended 5W20, and keep it changed frequently.
Both the 3V ("tritons") have variable valve timing,, which is what helps provide the better HP / Torque and MPG, at the expense of costing more and being more complex.