This sounds like a Ford aftermarket alarm (dealer installed)as Ford does not have those buttons and twisted wires from the factory as you have described! You can disable it however if you are using the remote key fobs that came with the alarm, you will need to acquire factory key fob in order to be able to unlock the doors remotely! You will need to Unplug the connector to that IR module that you saw, or remove the inline fuses that go to it! Now the only other thing that you must do is locate the wire coming from the ignition switch that would have been cut and wired into the alarm, this wire is the starter signal wire! You will need to locate both halves of this wire and restore the factory connection back to the same color wire, which should be a red wire with a light blue stripe! You should see a non factory butt connector within 8 inches or so of the ignition switch on the steering column! Below I have attached an illustration of the ignition switch connector and highlit the pin location for this wire, locate the wire at the connector and follow it to the place where it has been cut, cut it here on the alarm side of the butt connector to give you the needed length to make a new connection, then locate that same red with a light blue stripe wire where it would be connected to another wire of the alarm module, cut it at the butt connector and restore the red with light blue stripe wire to the red with a light blue stripe wire! I hope this doesn't sound to confusing, sometimes things are difficult to explain without being there first hand!