P1316 and p1754

[carterjf2]

Please help I have a 99 7.3 powerstroke that has the following codes P1316 and P1754 the first one is causing the engine to run rough and i have changed the IDM, changed the PCM, put new wires in under valve covers and replaced the engine wiring harness that plugs into the valve covers, still the same problem runs for about 30 seconds fine when CEL is reset then it starts to run rough again. No other codes like a fuel pump or low pressure, the second problem is a coast clutch solenoid code that flashes the transmission o/d light yet shifts just fine according to ford and the transmission shop. I do not know if it is just a chaffed wire or something else. Your help would be appreciated. Should I change the entire underhood wiring harness?