One way I improved the throttle response on the '04+ 4.0L V6 was to remove the plastic throttle body spacer. It has some little "teeth" moulded into it that allow a smoother transition from closed to tip-in throttle. Thing is, these vehicles don't need a smoother more gradual transition to tip-in...They need an improvement in such.
By eliminating this little spacer and replacing it with a standard fibre gasket, there's no more restriction at light throttle openings, which equates to a somewhat more responsive feel in the throttle response. It's getting more air quicker when the throttle is opened.
The mod is simple, and should take all of 10 minutes. It's only for the 4.0L V6, not the 4.6L V8...The V8 doen't have the same design.
First, remove the throttle body from the intake plenum, then remove the spacer/gasket. Install (1) Fel-Pro #61050 throttle body gasket* in place of the spacer. Installing the throttle body with the original bolts will require a couple washers on them to make up that difference that the spacer took up. Otherwise, it's possible to bottom out the bolts in the plenum and possibly split it. On mine, I got some new bolts that were about 1/4" (~4mm) shorter to give it a more finished look, but two or three washers on each bolt will accomplish the same thing.
The difference is quite noticeable, especially when rounding a corner and getting back into the throttle, the response is much better. These trannies still don't have the quickest downshifts and sometimes seem to get a bit confused as to what gear to be in, but aside from that, I feel it's a worthwhile mod. I also like the extra little "swoosh" noise when the throttle is just tipped in. It's very noticeable with an aftermarket intake or even a K&N drop-in filter in the stock airbox. With a standard paper filter, it's there, but much more muffled.
Considering you'll have less than $2.00 USD invested in this mod, it's definitely worth a try.
*Order the throttle body gasket for a '99 F150 4.6L if you can't get this exact brand or your parts store requests a vehicle application.