Are you datalogging the car? You have anything to look at? Are your knock sensors still active and enabled? When I was first tuning my 01, the knock sensors would become active at 4k and higher (This is with a Novi 1000). Ended pulling timing at .5 degree increments up to a total of 5.5-6 degrees by 6300.
Definitely noticed something was up after a few highway pulls.
Have you datalogged pressure drop across the injectors? Most of the Cobras (not 03-04) I've seen with blowers and 03 Cobra tank and pumps need an adjustment to the tune to keep the pressure drop where it should be. This could be part of the problem - also what is the duty cycle of the fuel pumps?