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Here is a TSB on a calibration update to fix alot of your problems.
This article supersedes TSB 9-7-11 to update the model years covered and Integrated Diagnostic System (IDS) calibration level.
Some 2003-2007 F-Super Duty vehicles, 2003-2005 Excursions and 2004-2010 E-Series vehicles, equipped with a 6.0L diesel engine may exhibit hard start, no start, white smoke, lack of power, running rough condition after cold engine start up, or diagnostic trouble codes (DTCs) P0404, P0470, P0611, P1260 and/or P1378 issues. Refer to the Calibration Content for information detailing specific vehicle content by vehicle application and model year that is being addressed by this calibration update.
This article includes previously released calibration content that improves injector performance in cold engine operation and additional diagnostic capabilities and product protection strategy enhancements. These enhancements provide additional diagnostic capabilities, adds additional new DTCs and engine protection strategies. Refer to the Calibration Content for additional details. See the appropriate Powertrain Control/Emissions Diagnostic (PC/ED) manual for technical descriptions and diagnostic routines associated with new DTCs.
Reprogram the powertrain control module (PCM) using IDS release 63.13 and higher or 64.01 and higher. The transmission control module (TCM) and fuel injector control module (FICM) , will automatically update if they are not at the latest calibration level. This new calibration is not included in the VCM 2009.11 DVD. Calibration files may also be obtained at www.motorcraft.com.
Reprogram the PCM to the latest calibration following Workshop Manual (WSM), Section 418-01.
The PCM and FICM calibration update contains improvement actions to address the following symptoms:
Previous released calibration content included in IDS software release 48.2 or higher for: 2003-2007 F-Super Duty, 2003-2005 Excursion and 2004-2008 E-Series 6.0L diesel equipped vehicles:
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P0341 is a cam sensor possibly acting up
P0401 normally indicates a bad EGR valve
P2285 indicates a bad ICP sensor or connector