Maple Leaf Rag by Scott Joplin

Here is an example piece typeset in MuseScore. Mostly done, but there are a few strange things which someone might be able to comment on:

1. measure 43/44: There is a clef-change at the end of measure 43. But there are two clefs given in the music. This may be due to the structure of the MusicXML used to initially import the notes into MuseScore. If I delete either one of the treble clefs, the music after the clef reverts to bass clef. This is also true of a few other locations in the music (m9/10 and m47/48).
2. In m52, the organization of the notes in the chord is not right (The bottom B is on the right side of the staff rather than the left where I want it). Also, the C just above it is not attached to the chord stem. This strange arrangement occurs on other chords when I try to move the beams (such as in measure 53).
3. The last measure contains three eighth notes. These notes are not aligned between the left and right-hand staves.
4. During playback, musescore seems to be confused with first and second endings, and sometime skips the repeats. Perhaps this is due to the import of data via MusicXML?

Attached is the MuseScore file, a PDF result from MuseScore (printed in 0.9.6.3 in Windows XP), and scans of the original typesetting from the first edition for reference.