With the 4.6L, you really can't do much performance wise without spending huge amounts of $, in which case, it would be less to swap it out for a low mileage 5.4L unit.
One thing you can do, is to better harness the power you do have. For about $500-750 (RWD/per axle) you can swap out the stock gears (3.55/3.73 and even 4.10) to a 4.56 unit. This will give you better take off performance and even better mileage around town due to the lower gearing. It'll lower highway fuel economy slightly (1-2mpg), but just by lowering the axle gear you should be on par with a stock 5.4L with 3.73 gears.
A programmer for the 4.6L won't net you much power. As you've done a few mods already, I'd do the gear swap and spend $400 for a custom tune, to make sure you maximize the performance from your mods. I'll also mention that be sure you don't want to add any more engine mods, or the custom tune won't be as efficient. Programmers can only do so much, but a custom tune such as BG Tuning, is a good one to go with. So, for about $1200, you can do the gears, and get a custom tune which is one of the better deals out there for the 4.6L.
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