Resolution: finally found a dealer who would look at the car. Misfires were fixed immediately with the misfire correction Phil mentions. That left the crank & cam position sensor codes. The shop says: "CKP not properly calibrated. Followed pin point test and realigned CKP sensor. Removed serpentine belts and pass side axle to access TDC port on crank. Rotated engine to TDC and aligned CKP sensor with the TDC tooth on crank pulley. Using Ford special tool and WSM specs, cleaned out oil from CPK connector." So there were no actual malfunctions, all the bits simply weren't cooperating. Runs great now, but what an ordeal getting to this point!Try doing a "static misfire correction". Usually done with the dealer tool. There are no EMI issues with the install are there?