If this is a stock alarm this may work. Here's a trick to disable the stock factory alarm. Unplug the engine hood courtesy switch harness, and connect the two wires together. This will trick the alarm ECU into thinking that the hood is open and won't arm itself.
It is E6 in this picture:
If it were my car I would try to keep the stock alarm functional. When I first got my car and accidentally set the alarm off to the point where it wouldn't start; all I had to do to return it to normal operation was lock the car from the inside using the inside door lock switch (while the door is open so you can get out), get out and close the door, then unlock the car from the outside using the key on the passenger door lock. Stupid but it always worked for me.
Edit: I just realized that you have a new door lock assembly from a donor car so my trick won't work unless you have that key. Can't you switch out his old lock or get a separate key using the VIN on the replacement door?