1. Yes, that would be a lot of work, and it's not my recommendation because it's usually better to work with rather than against the app functionality.
2. You can still start/stop auto-scrolling manually if you prefer, but you should start it when the song starts and let the pre-roll do its thing. This would give the same result but would be easier than removing the pre-roll and then manually starting auto-scrolling after some time passes.
3. You can add markers to PDFs, too.