- Starting on non-overlapping stems in chords issue. It should only be a problem when a new voice starts. If a voice stops mid bar it might indicate a problem too.
- Each stem in a 'chord' much be a different voice. In the two examples in Rev Etude, both 'misplaced' stems start new voices.
- Done. Here's a pic of the example in the Rev Etude. The dotted minim caused the problem.

- Starting on finding ties (such as those in blue in the pic above). I think ties/slurs/phrases are being found quite well already but not categorised yet.
- Ties apply to individual notes, not stems. Curve direction of tie doesn't relate to stem direction but does matter to note position relative to stem.
- Tie will overlap on X axis unless tie curves up in the middle and stem is upright (usually). If start or maybe end note are not the top/bottom note in the stem the tie may be moved to the side.
- Tie ends must have same Y.