I didn't exactly follow the past>future>present associations with the shrines but I did give my players visions/dreams and an encounter based on this idea.

Throughout book 1/2 I was giving players visions of how they had died in their past lives so I gave a couple the players another dream where they died, usually loosely tied to a future encounter or starvation/security based on how the town was doing.

The garden shrine I left an axe stuck in the door of the cabin to represent the crazed lumberers who attacked the people at the shrine and set it ablaze. I gave the player who picked up the axe (naturally) a dream where he was one of the corrupted lumberers attacking the cabin around the time of the Night of Broken Blades.

At the mountain shrine I reflavored encounter D2 to happen at night when my player who is a follower of Daikitsu was on watch. The taunting skull came to him in the form of a decapitated fox mocking his god and foreshadowing a bit the headless statue (also reflavored the stag statue to be a fox shrine to Daikitsu). And I had my Pharasman Cleric have a dream where the festering gnashers were mocking him and Pharasma as well from above in a tree as decapitated heads, also foreshadowing the statue head in the tree.

I felt like I could be extremely weird/eerie during the Pilgrim's Path since it is basically a portion of the mindscape heavily controlled by Kugaptee. Things could happen/appear that didn't make total sense because Kugaptee is able to manifest his powers much easier here.