It would be nice to see the 2 runs laid on top of one another - the WinPep software can do that and they typically save all runs. Your shop can also output them in electronic versions in color. This would be a much better way to show the increase as trying to compare numbers and slopes is difficult. A color scan of the printouts would also be helful.
The improvement numbers you mention are peak values and each appear at a different RPMs - the first thing that jumps out is at 3.8 RPM where one scan shows over a 25pt increase Then the downslope of the one with the intake is more severe.
Also, if this is the direct injection 3.5, the numbers will be noticeably different as your engine handles air and fuel differently.
Jay, Alpine designed their SC system to be CARB legal in all 50 states and the ONLY way to do that is to use the stock airbox. It is common knowledge in performance circles that increasing breathing (intake AND exhaust) is always a benefit and even moreso in SC'd or Turbo'd applications.