My file looks fine in MuseScore but when uploading it to RMS Coach^ it's missing parts.

MuseScore handles its MIDI exporting a bit differently than other programs.

This is a known MuseScore issue. To get around it, simply keep the first MIDI track in MuseScore blank. This will lead to all parts appearing as they should in RMS Coach.

The why of this is covered in this article. Long story short, Musescore treats MIDI Track 0 as an actual instrument track, where almost any other Digital Audio Workstation treats MIDI Track 0 as a conductor track.