HiCustomerthis is lostrider, the concern your having is due to the carbon deposits in the Electronic Throttle Body assembly, there is no way to clean to correct the condition, the Processor will have to be reprogrammed and the throttle body will possibly have to be replaced to correct the condition, here is a service bulletin for the problem your having, the only thing is the recalibration has to be done at the dealership due to they are the only ones with the equipment to do that, here is a copy of the service bulletin for the concern, hope this helps.
This article supersedes TSB(s) 08-5-13, 07-23-12 and 06-25-8 to update the Service Procedure.
Some 2004-2006 4.6L and 5.4L F-150 (excluding F-150 Heritage), 2006 5.4L Mark LT, 2005-2006 6.8L E-350 / E-450, 2005-2006 6.8L F-Super Duty (F-250 to F-550), 2006 6.8L F-53 Motorhome Chassis, 2006-2007 4.0L Explorer 4 dr, 2007 4.0L Explorer Sport Trac, 2006-2007 4.0L Mountaineer, 2006 4.0L Mustang, 2006 - 2007 4.6L 3V Explorer / Explorer Sport Trac / Mountaineer, 2006 4.6L 3V Mustang, and 2005-2007 Crown Vic / Grand Marquis / Towncar vehicles may exhibit one or more of the following symptoms: drive-away hesitation, loss of RPM on deceleration, difficulty starting, and/or idle RPM less than desired. Malfunction indicator lamp (MIL) may be illuminated with diagnostic trouble codes (DTCs) P0506 and/or P0505. These conditions may appear after battery disconnect, dead battery condition, or keep alive memory (KAM) reset. The symptoms may be due to engine deposits in the throttle leading to airflow less than desired.
Follow the Service Procedure steps to correct the condition.
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Here is the procedure,