I agree, re-gearing will make a bigger difference than anything else. The intake, throttle body and the chip you listed are all garbage.
Re-gear (front and rear of course) with 4.88 gears. If you have to ask if you can do them yourself, the answer is no. They should be installed by an experienced gear shop, and with new install kits. You're probably looking at anywhere between $1200-1500 total. Find a gear shop before you buy gears as they may charge you extra for bringing your own parts and not warranty them.
The cheapest prices I got for gearing/differentials was from Whayne at diffsonly.com, once you figure out what you need.
2006 F150 FX4 Super Crew - Bilstien 5100s leveled 2", 35" KM2s, 4.56 gears, Detroit locker, Eaton E-Locker, Traction Bars, AEM intake, Xcal 2
2010 VW Golf TDI 6MT