Since you're new to this, you might be best served by an incremental, cost-contained approach that lets you try new stuff yet feel free to dump it if it doesn't work out.
First, your speakers need to be freed from their bookshelf gulag. Set them on decent stands like Monoprice, which will leave change from your $100 bill. Listen to that and see what that does for your room. Change one thing at a time, then listen at length
Next comes a decent amp. Your little Yamaha is okay but not ideal. Get more power than you think you need and high current output which will help your current speakers and might well be required to properly drive your next pair.
Third comes a good sub. All bookshelf speakers need a good sub.
Then the rest will come in its own time. Enjoy!