Before you take your truck to the tranny doctor, try performing an APPS reset on your own:
APPS Reset Procedure
This procedure has shown to help 24 valve ISB engines. It is basically teaching the fly by wire accelerator on these trucks to reread the position of the pedal and it's limits. Most complaints this will help with is poor acceleration, improper shifting, bucking in 5 and 6 speeds. Has been known to increase fuel mileage in some instances.
1. Set parking brake
2. Disconnect negative battery cables on both batteries
3. Turn ignition key to run(to drain any remaining capacitors)
4. Let truck sit for 30 minutes( this is the recommended minimum)
5. Return ignition to OFF position
6. Reconnect both batteries and secure, not a timed event
7. Turn key to run position(not start) and depress accelerator pedal slowly all the way to the floor
8. Allow pedal to return to top position slowly
9. Turn ignition switch OFF
10.Release parking brake
11. Now drive the truck to your nearest Ford dealer and trade it in on a real truck. 
(I could not help myself)
Why on earth would any smart Dodge owner do such a thing?
(I couldn't help myself either)
If the APPS reset does not solve the issue and your feeling mechanically inclined enough, here's the steps to test to make sure your APPS has the proper output voltage and the steps to adjust:
Many have found that correcting the output voltage from the APPS sent to the PCM has increased the throttle response, and boost. This calibration also adjusts the APPS for wear.
Instructions:
Tools: Digital Volt Meter, T-20 Torx bit, #1 phillips, 10mm socket
With the key on, engine off you need to probe the APPS wire to see where the voltage is currently set at.
The best location to probe the wire is on the PCM (Power Control Module) which is located on the passenger firewall behind the air intake.
You want the C1 connector, this is the connector closest to the engine
You want the orange wire with a dark blue tracer which is pin #23 (Please use a suitable backprobing adapter for your meter lead, do not pierce the insulation as this can lead to water intrustion/corrosion.)
Voltage should be somewhere around 0.5 volts,
At this point the voltage reading does not matter, it just has to be accurately written down for later reference
TURN THE IGNITION OFF ON THE TRUCK
Remove the black plastic cover off of your APPS. There are two plastic screws. One on the top and one on the front facing the radiator. It takes a little prying to pull it off.
Undo the 6-10mm bolts that hold the bracketry in place but DO NOT REMOVE THE CABLES!!
You will notice the APPS is on the back of the bracketry that you just removed, it is held in place by 2-T20 torx bit screws. These screws have a little bit of locktite on them so make sure you have a good socket and gently give a little tap with a hammer before attempting to loosen. Be very careful because these screws strip VERY easily and you only get one shot at them (VERY VERY VERY IMPORTANT; They are VERY tight).
On the APPS you will find a white tag that gives you the information on what the APPS voltage should be.
After loosening the screws (do not remove) you can rotate the APPS clockwise or counter clockwise to get the adjustment (towards the front of the truck increases voltage and towards the rear of the truck decreases voltage)
The reading you took at the beginning of the process on pin #23 should match the white tag on your APPS. If it doesn't the adjust accordingly.
