#3 is for the ambient light sensor. Not needed for startup, but it is fun to be able to tell people this contraption you built has automatic headlights.
#4 might be one of the ignition switch plugs?
edit edit: I think #4 is the Ignition Lock Cylinder Control Solenoid. Should be right around the ignition switch.
Not sure on the first one/two as I had a different donor. Wire colors and the year of your donor might help others.
edit: crankshaft position sensor is a three wire sensor on the front of the block, and is grey, brown/white, and pink/black, at least in an '06 LSJ.