Why would you need to change the harness if you could just move the pins to the right locations? The ecm connectors are the same. Same goes with the valve cover. There are still only 2 wires to each injector in either system. Who cares if there is 3 plugs or 2? Also, why would you need to change the pedal? The ecm is only looking for a voltage for TP right? Then just connect the proper wires for the CAN bus to the OBDII.
Sounds like you agree with my thoughts earlier buddy, I'll print out the pin outs for the 06-07 CAN ecm versus our 03-04 SCI's and see if there are any conflicts. This may be an easy swap, or not, lol.