Well, It's a VN game right? As long as the dialogs are clear enough a normal player should more or less have an idea of what to do. Another thing you can try is for example: If another character said something relevant (that can be the hint for the player) you could play a small distinct sound sample with a little visual effect. Something similar to Metro 2033's karma system.
Another thing could be a small pop up like Telltales 'The Walking dead'. ('X character will remember that'.)But saying thing's like 'Hope you payed attention to that.' or 'Did she meant X thing from Y.' Something like showing the player's though.
And my last idea/suggestion. A journal. Literally, pressing J or a book icon to access a small list of relevant clues, item's descriptions and etc.
Something like these? Sometimes there's no need to reinvent the wheel.