Well I'd definitely look into a computer reprogrammer if I were you. I have a Hypertech Power Programmer for my 5.7L Vortec powered GMC and it made a big difference in acceleration just by altering shift points and shift firmness. I'm still playing with the power tuning features of the programmer so I'm unsure of increases there but I've heard really good things about it in reviews. I also added a Flowmaster cat back exhaust and gained a little over 1 mpg. Not sure of any power increase because I didnt dyno test before and after but it sure sounds bad@zz.
Electric fans are a good idea but I'd shy away from power pulleys if I were you. Especially if you're running any kind of stereo system in your truck. Nothing more annoying than dimming
headlights while idling. A well designed cold air intake will help alot but make sure you get a good one not one of those from a company that spent all its money on chrome plating instead of R & D. You might want to try building a ram air for your stock air box, sometimes those are just as good.
Not to offend you or anything but I test drove an '02 5.4L Ford and it was the most anemic truck...salesman said computer tuning really wakes the Fords up. Hope your it does the same for your 4.6.