From your description it seems to be an electrical or sensor problem. It really sounds ALOT like wiring harness chafing. All the symptoms are there. Did the Tech specifically state he checked the entire harness? Has it had the 06E17 flash? Could also be a combo of problems including sticky turbo vanes.
Chafing:
Wire Chafing Issues:
A variety of driveability issues can arise from chafing/shorting wiring, such as crank/no-start, stall, running rough, misfire, buck/jerk or lack of power. The most common location for this is the valve cover/cover bolts near the FICM or the intake manifold bolts where the harness routes under the air intake hose. The harness should be rerouted and any chafe points insulated with rubber vacuum caps. Other chafe problems can occur where the sensor harnesses route around the valve covers, thermostat housing, idler pulleys, glow plug relay bracket, and near the accelerator pedal assembly (adjustable pedals), and also near the PCM by the battery and near the relay box brackets at the left rear corner of the engine compartment. On Econolines, also inspect at the top edge of the computer, along the oil dipstick tube bracket and auxiliary A/C lines. Broadcast Messages 1407 and 3077.
More harness info courtesy of the Ford Doctor: www.forddoctorsdts.com/articles/article-05-11.php
Flash:
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.