One thing to remember is that an RPG is not a book or movie! For the most part, and RPG is a story where the player characters are the main characters.
When I was younger, I found that anytime I tried to get "clever," I would lose players. This did take time to sink in, but it eventually did.
When foreshadowing, be very obvious, but aim it at the big bads employees, and enterprises he controls. For example, maybe a gain that he secretly controls is killing the big bad's enemies. The players concentrate on the gang. Then one of the big bad's lieutenant's embezzles a lot of money. The big bad's wife is cheating on him and then dies in an accident.
As for clues, I not only agree with the three-clue rule, but I use the rule of obvious clues. If there is a clue that the characters must find to continue the adventure and they aren't searching for a secret safe, then put the clue somewhere the characters are searching. Maybe they search the desk instead, and reveal the clue inside a secret drawer that they automatically find. (I don't require rolls for things that a character would automatically do.)
I try not to overestimate the abilities of the players. Perhaps the character is Sherlock Holmes, but the player certainly isn't.
Another rule I have is to never build an adventure that requires an NPC to solve things. If none of the characters is a detective (or equivalent) I save my mystery adventure for a later time. I'll provide an NPC only if the characters hire one, and this NPC will never be better than the characters except in his one area of expertise. If the characters hire a detective, then he will be a average detective at best.