I'm still not 100% on the map, but here's a sample of the kind of clue players will run across in the Ancient Tower. I'm thinking that there might be a sequence that gives an explanation as to how this type of clue is a clue. Most probably, this sequence will happen after reading one of these plaques for the first time. Of course, I will not outright tell players the answer, but hopefully, I can give them the direction they may need.
Maybe, I should have the explanation sequence optional, though? That seriously just popped into my head as I was typing the above text.