AE is Auto Engineuity. It is a program you load onto your laptop, plug it into you OBDII sensor, it tells you pretty much every thing you ever wanted to know about your truck. You can pull numbers, post them here, we can pretty much tell you what the issue is.
My comment was sarcastic. Matt tunes with a smooth pedal, the harder you push, the more power you get, it does not all come on in the first 25% of pedal travel. Some people think that means you are not makeing power, what that actually means is that you have much greater control of when the power comes in or out. A bumpy road will not make your truck jump up and down in power. It is one of the nice things about having a throttle pedal that is electronic as opposed to a mechanical link.
Time yourself through a WOT run 0 to the speed limit (would not want you breaking any traffic rules), see what it does.
Best place to get said program. Dennis rocks.
http://shop.strictlydiesel.com/store.php/products/Autoenginuity