Chapter 05 saw the problems and stopped there. This is the other half: you fix a mostly-correct map by hand. The two layers built separately finally operate together — an accidental extra beat in a 4/4 bar is invisible in pure tempo terms, only the meter overlay flags it. Bars with the right beat count glow green; bars with the wrong count are flagged with the actual count. Drag a marker to move it, click a marker to select then press delete to remove it, click empty grid space to insert a beat.
bar with the expected beat count bar with the wrong beat count pickup / trailing partial beat (orange = selected)
The download is exactly the format beat_this produces, so it's a drop-in replacement for the file you uploaded.