It seems to me that you turning WAY too many RPM's for a basically stock motor. Have you had the car on a dyno to see what the power band looks like?
I just found another thread that backs up shifting at that RPM. If iam understanding it right you should shift 10% above the max power. So on a 96 cobra the max power was at 5800. This puts the shift point some where around 6380. Thanks for bringing that up it got me searching in the right direction I think.
No guessing about its the only way to really know......From the way the post read you should shift at 10% higher because you are still making more power at that mark (Say 5500) than you would make at the lower RPM you will hit by shifting. I guess the only true way to know shift points would be to have it dynoed and get the HP at each RPM and than look to see were it is most efficient to shift. I now know that 6900 is for sure to high.
+1...........I have to agree with Bkid......
If you loaded the stock tune back in and it performed better given the same parameters, it is in the tune. We hate canned tunes.......
Strap it on the rollers, and find where your power curve is once you get the tune fixed.....