I've decided to start some modding on my truck. 2003 with the 4.6L in it. Its completely stock and I don't really know where to start first. I was thinking maybe a programmer to help out the gas mileage. Or would some long tubes and bigger exhaust be a better first step?

 

If gas mileage is your concern, there may be 1-2 mpg?? to be had through tuning.....so I've heard. A $ 300-400 investment would take forever to pay you back when compared to that possible fuel savings. So, keep her stock and do the best possible maintenance.
If you want a better running truck which is more enjoyable to drive, good tuning is more than worth the money and a great place to start.