I don’t entirely agree with the gearing theory, because a six speed has lower gears in first. But it really depends on the OP’s perception at this point, and we have no idea if he’s feeling this based on 0-60; 40-60; or track times LOL.
It may be nothing other than a perception based on a difference in throttle response. People buy throttle response tweaking devices all the time and convince themselves it’s improving performance when all it did was give them 80% of the output at 40% of the pedal.
OP, I suppose at this point the original truck is gone so you have no opportunity to run a comparison of the two with a stopwatch?
There are many things that can diminish performance.
And many things the previous owners of the ‘07 may have done to enhance it.