Where do I start (high EGT)

[Bob]

I have a 06 6.0L. It has had what I believe to be the latest flash. AFE intake, Banks technicooler inter cooler kit, Depaco 70 horse injectors, MBRP 4" exhast w/ 3.5" down pipe and an Edge Evolution. It seem to run good, but has some of the issues I have read about in the forum ie. rough idle untill warms up, poor fuel mileage, no low end power. And all these seem to come and go randomly, but my biggest problem is high egt. It takes nothing to get to that 1300 mark or higher. Sound like some reprogramming would help, but would the egr delete be something I should do first? I just dont know what to do or in what order.