I don't think we are going in the right direction (as a society) to continue using CID, instead of Liter Dispacement as our standard. (Damn Europeans!)
My vote (why didn't we get to vote on this????) would be for the 5.4l based combo. You have to compare apples to apples or oranges to oranges, though. There was never a supercharged version of the 351w, so the rods (and other things) that came from the factory would not be considered equivalent to the SC 5.4l. These two engine were built during "different times" and therefore have different intended uses.
In the same state of tune, the same design intentions and the same hp level, the 5.4 based combo just barely eeks out the 351w. The reason...fewer moving parts (not to mention 30 + years of engineering). Overhead cams. Lighter valvetrain=less chance of floating valves. Although there are ways that the 351w could easily do this, it would be >slightly< simpler to have the benefit of the extra engineering, in the 5.4. Plus, there are already guys out there making 800hp with stock block Cobra's and Lightnings.