But the bar numbers displayed in your DAW as the audio file is playing can be misaligned with the bar numbers shown in the sheet music.
Again, I don't understand why that affects you playing along with a song. Are you not just reading a chart? A real chart, like dots on stave paper? You listen to a music file, not watch it. You watch the sheet music.
How about a video clip of what the puzzle is? At least a still pic.