This is huge issue. The problem is a faulty Fuel Injector Control Module (FICM) every time. It's such a problem that Ford has issued a bulletin. Here is a copy of it.
Best of luck
TSB 08-26-3
01/05/09
6.0L DIESEL - DRIVEABILITY - NO START, HARD START, RUNS ROUGH - FUEL INJECTION CONTROL MODULE DIAGNOSIS FORD:
2003-2005 Excursion
2003-2007 F-Super Duty
2004-2009 E-350, E-450, E-550
This article supersedes TSBs 04-18-6 and 07-5-4 to update the repair sequence FICM_MPWR check, symptoms and additional diagnostic information.
ISSUE
Some 2003-2005 Excursion, 2003-2007 F-Super Duty and 2004-2009 E-Series vehicles equipped with a 6.0L diesel engine may experience no starts, hard starts or rough running when cold and may be accompanied with diagnostic trouble codes (DTCs) P0611, P1378 and! or all 8 injector circuit codes. These symptoms may lessen or disappear when the engine is warm. These conditions may be caused by the Fuel Injection Control Module (FICM) or injector spool valve sticking internally during cold engine operation. ACTION
Follow the Service Procedure steps to correct the condition.
SERVICE TIPS
A failed FICM module can cause diagnostic trouble codes related to injectors even when the injectors or injector wiring are not at fault. The FICM module should be checked for proper operation before evaluating injector operation or wiring issues.
For information: Symptoms of stiction (These conditions are caused by the injector spool valve sticking internally during cold engine operation engine oil temperature) can be improved by using the lightest possible specified weight oil during winter months. Refer to the Owner Guide Information - Diesel Supplement / Maintenance and Specifications / Engine oil specifications. After confirming that the appropriate weight oil is being used, evaluate the injector operation according to Step 13 of the Service Procedure.
Information On The FICM TEST:
An improperly operating vehicle battery(s) or charging system can cause additional operating loads to the internal components of the FICM module, due to low power supply voltages. Glow plug operation, vehicle accessories (factory and non-factory installed), and hot and cold temperatures can also put additional requirements on the vehicles electrical, battery and charging system. This can result in shortened FICM module component life.
The FICM module contains two major internal components, the main circuit board and a DC-DC converter. The DC-DC converter is the device that amplifies battery voltage to 48 volts (V) to operate the injectors. Two major test entry conditions listed below are critical to accurately test the FICM DC-DC converter:
Engine Oil Temperature (EOT) Less Than 68 °F (20 °C)
The calibration in the FICM uses a pre-cycle mode during Key On Engine Off (KOEO) / glow plug operation. This mode is used to rapidly heat the injector spool valve and prevent sticking during cold operation. During this mode, the electrical demand on the FICM DC-DC converter is near maximum.
L_PWR >= 11.5 V
The target 48 V output of the DC-DC converter is directly affected by the battery supply voltage, or B+. This is measured internally to the FICM with the FICM_VPWR PID. Ensuring both of the above criteria are met before conducting the FICM_MPWR test will prevent incorrect readings, misdiagnosis and replacement of good parts.
SERVICE PROCEDURE
1. Verify the battery and charging system are functioning properly. Refer to Workshop Manual (WSM), Section 414-00 for diagnosis and repair. If the battery cannot maintain a good charge, it will affect the operation and testing of the FICM, as the FICM is an amplifier and has to work much harder to compensate for low battery voltage.
2. Install Integrated Diagnostic System (IDS) and retrieve the FICM calibration information by selecting: ^ Toolbox
^ Powertrain
^ OBD Test Mode
^ Mode 9
3. If the FICM contains one of the following files then it has already had the Inductive Heat calibration installed: ^ ARZ2AH00
^ ARZ2AL00
^ ARZ2AL01
NOTE RECORD FICM CALIBRATION NUMBER PRIOR TO PERFORMING PROGRAM MODULE INSTALLATION (PMI) AS IT WILL BE REQUIRED LATER IN STEP 11. 4. After checking the FICM calibration info, perform a PMI on the FICM. This should be done even if the FICM already had one of the three (3) calibrations listed above.
5. Disconnect the glow plug control module (GPCM) power wire C1249A, circuit 361 (RD) from the passenger side battery. (Figure 1) This also disconnects the alternator to minimize power draw from the batteries and provide more consistent FICM testing.