Maybe you should have a qualified shop perform the necessary wiring changes.
Swap pins 9 & 42 back the way they were, they were there for a reason. Read your EVTM again. Pin 9 on the ECU side needs a constant power cause this is for the ECU's memory. Pin 42 is the yellow/white charge wire. Follow the alternator harness that has the yellow/white wire, it should come out to connector C149, the 12 pin plug under the abs module. You will connect the wire from pin 42 that you removed from the vehicle side and splice it to the yellow/white wire from the alternator at the 12 pin plug. You will then take the wire you cut from pin 42, splice another wire to it and ground this wire at ONLY a green stud on the body, or at the battery terminal. Any other bolt or screw is not a good enough ground and damage to the ECU could result.
SVT