Usually black smoke indicates an overly rich condition. Assuming the F250 is a MAF ran engine, a leak post metering will cause the black smoke/hesitation. Check all your couplers and make sure they are tight. Boost leaks could cause the same issue.
See attached picture-
These are known to rip, use a mirror to see behind/underneath. They have been known to also rip right at the clamps to where you can't see the rip, so you might want to remove the clamps to inspect boot.
In the picture you can see the blue boot top/right. The red hose in this picture goes to the MAP sensor, yours will most likely be a black hose. You can check that hose out for damage also, and while your at it clean that black hose and brass fitting in the intake. Some times soot will block up the hose and fitting.
Have you noticed any black soot in the engine bay? You may also have an exhaust leak. Check the turbine exhaust housing and manifolds.
2003/04 Computer Programming Recall 06E17:
Truck built before 9-29-03 are being recalled to have the computer reprogrammed. The reason for this recall is to correct fuel injection timing during cold operation, EGR valve control, lack of power, check engine light illumination (P02263 or P0299), hard starting and rough running concerns related to Exhaust BackPressure sensor corrosion. Other symptoms not listed in this recall, but which could occur, would be excessive smoke, turbo control and surging at idle or cruise. The new update eliminates the EBP sensor input to the computer. The exhaust backpressure will now be inferred/calculated using other sensor signals. Trucks should be reprogrammed using versions 41.8 or 42.1 or higher.
After this reprogramming, the truck should be test driven, the computer checked for a codes and the codes cleared (even if none are present), the key cycled on for five seconds, then turned off twice, then the engine started and allowed to idle for 5 minutes at operating temperature to allow the computer to relearn the EGR valve closed position value. This is to prevent erronious codes or driveability sysmptoms related to the EGR valve an turbo performance. Broadcast Messages 5452, 5529.
You should notice an increase in turbo cycling closed/whistling at idle and at stops. This is normal, and is to help keep the variable vanes from sticking.
I am also wondering if the vanes in the turbo are potentially sticking? If so they will need to be cleaned.
Tuesday, January 29th, 2013 AT 9:24 PM