Use
var newTroop : GameObject = Instantiate( troopObject );
newTroop.GetComponent(WayPointScript).target = clickedTransform;
Then newTroop will be set to your newly instantiated troop object.
Use
var newTroop : GameObject = Instantiate( troopObject );
newTroop.GetComponent(WayPointScript).target = clickedTransform;
Then newTroop will be set to your newly instantiated troop object.