You cant use the bonne PCM, so just get yours flashed or grab a 99-02 GTP pcm.

Get the motor and the trans out of the bonne, and be ready to grab up a few parts that are different between the 2, such as some of the dogbone mounts, supercharger tensioner bracket (or make a customish mount setup). You will also need a GTP pass side axle. Wiring wise you will need to swap your injector connectors out for EV1 connectors, and swap the map sensor connector or get a series3 map sensor.