The tuner should be able to get around the limitations of the stock computer with no problems. Heres the picture of the printout that Fox-4-Cobra emailed me. The place he dynoed at wouldnt send him the whole file.
The only thing that stands out to me is that the numbers are low. It looks like its holding the power pretty decent before he stopped the pull. You cant tell exactly what the air-fuel is, but it looks like its in the 13.5 range.
With flat-tops and 93 octane, 28 degrees is about all those chambers want for timing. I dont think thats the problem.
I'd really like to know exactly what the injectors were doing. From there I'd look at valvetrain geometry. Also, what spark plugs are you running? The next time you go back to the dyno, take a 3.5" floppy and tell them you want the files saved to it, otherwise you will go elsewhere.
Andy