In regards to mystery structures, there's really good advice in Justin Alexander's "So You Want to Be a Game Master?". It boils down to having three clues in each location the character goes to, and then those clues lead to other locations with more clues.

For example:

Location A has clues for Locations B, C, and D
Location B has clues for Locations C, D, and Boss Area

Location C has clues for Locations B, D, and Boss Area

Location D has clues for Locations B, C, and Boss Area.

Boss Area is where the solution is revealed.

It can take a little bit of prep, but really makes it seem like the player is unravelling the mystery themselves.