Thanks for the quality feedback! Scoring went through a few iterations, but ultimatelly, you get 10 points for hitting a note, lose 5 for missing a note completelly, and then also gain... I can't remember the exact values, but about 0.1 points for every 0.1 of a second when holding the right note, lose about half that if holding a note which should not be pressed. There was no system to verify if the note was hit perfectly or little late, so yeah, there is no punishment for hitting the note after 90% of it is over... apart from losing the note-holding points.
I've played through these songs probably about a 100 times readjusting the notes to fit well between following the music perfectly and... being actually possible to play, so uhh no wonder I'm still near the top of the leaderboards :p Looking back on the feedback we got (including Yours), the notes should have evolved a lot more between the songs, to improve the difficulty curve and lessen the sense of repetitiveness...