A 2001 and earlier will have a dome light above the rear window. So the top harness will have the 2 wires associated with the lamp (pink/white and yellow). The pink/white is hot always. The yellow is a switched ground controlled by the instrument cluster, which is controlled by the door switches. This lamp was eliminated in 2002 so your 2005 will not have those wires in the top connector.
IIRC, your post said 5 wires on the 2005. There will be a large black = ground, large black/white = rear defrost from switch, brown/light green = rear wiper motor from switch, and two brown/pink - one of these will have voltage when the key is turned on, thge other will not until the connector to the top is connected. This is to prevent the rear washer from activating unless the top is in place and connected, it also provide power to the rear wiper motor for "parking" of the wiper arm. The colors i've quoted are from a 2003 FSM. I do not have a 2005 FSM sorry.
If the colors differ, the two large wires in the 2005 side will be for the rear defrost, the two of the same color will be the "power" to the rear motor/washer control as described above.
If your top has the dome light, this can be wired in, just locate the correct 2 wires under the dash on the left and run this wire to the top connector. I also added a small switch so I could light the rear dome lamp without opening the doors. PM me for details.
If you're really into change, order the 2005 hard top harness (56009377AE) and change the wiring inside the top. This will give you the correct connector at the rear. This assumes the connectors at the rear wiper motor and rear defrost inside the top are the same from your top to the 2005 year. That part number is for a TJ ( not LJ) and has a list of $94.35.
Go to http://www.trademotion.com/partlocat...&siteid=213951
to buy this harness for $70.76