Mystery Design in TTRPGs

For the Pathfinder First Edition game that I ran, I introduced mystery elements. Below are the various diagrams and mind maps that I used to  figure out the plot for most sessions:

First is the rough timeline of events for each session, in order.

Since this was also a mystery game, with player-lead investigation, I also had to give the players clues as to what they were going to be encountering during the session. Below are my notes as to what hints I should give: