First of all - did you turn TC off? Secondly, did you turn off the OD? If no, that could be the prob.
Nextly, keep in mind that your Perilli's are fairly soft.
When they're cold they can "chirp", but if it's hot outside, streets are hot, or the tires are whot, ththe Perillis sometimes make a more subdued scratching sound on the pavement. regardless or that you should hear something, and feel a much stronger shift - but IMO you are shifting about 400 rpms too early though...
When I was stock and did the tune and intake I was definatly running to redline - but I leave shifter in 'D' and tranny is programmed to hit the 1-2 & 2-3 shifts hard enough to hear them.
I think the important question here is do you notice any obvious diff in how it runs? The automatic cars seem to benefit the most from programming because so much of it is with the tranny. If you're not getting a noticible gane, try evolution, tillman, or brenspeed.