Like Spirit Lamp said linear interpolation is the best way to determine a notes position. I'm working on a rhythm game tutorial for Unity to be uploaded before the jam, so by the time its out you may be able to take some concepts and convert the code to GML. I do agree that explaining everything programmatically is difficult so here are some visuals.
For linear interpolation you would do something like
Note_Position_Y = Lerp(NoteSpawnY, noteTapY, timeSinceSpawned / noteTime);
I hope this helps