The author definitely foreshadowed too hard for this sort of long game. The clues don't seem to contribute towards any one overall picture and instead each clue branches off into a whole different direction and also away from the main problem of Tsubasa-chan. The heavy foreshadowing of each girl also is too much, especially when the MC doesn't seem to get none of it or question anyone who's diving into this big problem with him.
Even the 'hints' that are dropped aren't purely from the actual clues but rather someone near him interpreting the clues in one specific way and leading him down that path.