I have been in the second map area and have a journal entry for the totem of defiance that tells me I should look for clues. I have looked this up online as I'm at a loss as to how to get the clues.

It seems that I should have bought the clues item from the Farmers Market merchant before carrying on with main quest. As that merchant is no longer available to me I followed online advice to get the clues item from the Costal Farms merchant.

It would seem I am now stuck unable to purchase that clues item - no spoilers as such but the original merchant is gone and the alternate merchant has not got the clues item for sale.

Online sources suggest that the totem pieces can be found without the clues but I thought it best to purchase clues as I did for first area totem [was still difficult to track pieces - but all part of the fun] - I would rather follow the clues in game than use an online walk through.

If any one knows another way to get the clues such information could be useful to me and others in the same situation - no clues means randomly looking for something without really knowing what to look for.

I do not know if this has been overlooked by the developer and is an accidental issue or if there is a bug preventing purchase of the clues item.

The merchant will be relocated to the Abandoned Farms after the spoiling event you referenced. 
 

Although it seems like waiting until after that event breaks the quest.  Can confirm the Idol of Covert Plots is missing from its location. 

Update: can confirm all totems pieces are missing. Looks you have to complete this before the Naku Tedek quest.

 

Total bummer.

I'm having issues with the Totem as well. I bought the clue item early into the second area, but pieces of the Totem are unattainable on multiple saves.