I did this after the main story was over and was in free roam mode. You can also pay teleporter ninja 1000 ryo to teleport you to different locations including the other villages. You do have to walk the paths anyways though to get all the timeline pages.
Villages to visit:
Village Hidden in the Leaves
Village Hidden in the Clouds
-Go right, out of the front gate of The village hidden in the leaves.
-Through the training grounds
-Get to the Docks, tell the man to take you to the western land of lightning.
-Go up the stairs.
-At the intersection turn north and take the right path.
-Follow the path until you see a fork in the road next to a waterfall.
-Take the Northern route and then cross the bridge.
Village Hidden in the Sand
-Go left, out of the front gate of The village hidden in the leaves.
-Into the desert
-Keep following the path until you see the entrance gate.
-Head through the entrance gate.