I am in the middle of a swap. I was able to pull the engine wiring harness off with the motor. Disconnect it from the computer and start un-plugging things. The only wires I had to cut were the leads the the fuel pump.
The wiring harness coming off the bulk head stays plugged in to the bulk head and doesn't need to be removed. There are plugs from it that need to be dis-connected from the motor.
Take your time and disconnect everything. Once you start to pull the motor, you will find a couple more! Take a look at my build thread,I talk about the wiring. I will be firing mine up in a week or two!