The folks at Motor Trend did some sleuthing recently, and uncovered the reasons for an interesting mystery. Ford themselves claim that the horsepower for the GT350 and the GT350R are the same, yet the GT350R is a bit faster, besting its "non-R" sibling in a number of tests. They thought, "What gives?," and decided to throw the cars on a dyno and do some math.
It turns out that Ford's identical horsepower rating was legitimate; however, because the GT350R has lighter wheels, it can turn in better numbers, and effectively cranks out a tiny bit more horses because of it. That wasn't all though. Apparently, ambient air temperature at the wheels was also accounting for some of the improved performance. Here's a quote with additional detail,
There you have it. Apparently, this testing helped to alleviate the Motor Trend editors' concerns that Ford had given the R a "special tune."The ambient air temperature was to blame for that significant difference. Before we installed a sixth (!) fan to blow cold air directly at the intake, the Mustang's computer reported intake air temperatures over 115 degrees. With the fans, both cars provided consistent results with intake air temperatures around 100 degrees.
Additionally, the shape of the curves is so similar that it's hard to believe there's any tuning difference between the two engines—and indeed watching the ignition-advance curves, the two engines were doing the same thing at the same time.