Tiger
If your problem is, in fact, a common versus split staff problem, as Michael (SeaGtGruff) suggests, then correcting that should be "reasonably" manageable. Other notation software I have used will do this for you by converting a treble-only staff to a Grand Staff and automatically moving notes below Middle C from the treble staff to the bass staff. I am not familiar with MuseScore, but I did download a copy. To begin with, its editing capabilities are much more sophistcated than I expected, but sadly, it does not appear capable of doing an automatic treble-only to Grand Staff conversion, but it will allow you to declare separate treble and bass staffs on a new project, so that should make a manual correction to your current and future projects possible. To do this, you are going to need sequencer (DAW) software. If you do not already have that, I would recommend Anvil Studio. It is available as a free download from "anvilstudio.com". You would need to import your existing song file into Anvil Studio and use its track copy feature to clone your existing "track" into an identical separate track and decide which track you want to use as the treble track and which for the bass track. You would then do a batch note delete to remove all notes below Middle C from the treble track and all notes Middle C and above from the bass track, and save the file. Then, in MuseScore, open a new project and establish a treble staff and a bass staff and have it import treble track data from your file into the treble staff and bass track data into the bass staff. If you want to record a new performance directly into MuseScore and your keyboard has a "split" feature, you should be able to split the keyboard at Middle C and assign the upper zone to one MIDI channel and the lower zone to an adjacent channel, then tell MuseScore to record data from the upper zone channel to the treble staff and data from the lower zone channel to the bass staff. It appears that MuseScore can be set up to do this. Keep in mind that ANY notation software will have problems with left hand notes and/or right hand notes that cross over the split point, as the software has no way of knowing where those belong. For those notes, you need to use the software's editing features to move those notes to their proper ledger lines above or below their associated staves. I have had many years practice at this in helping new owners of Casio keyboards with "learning" features convert downloaded non-Casio MIDI files into compatible split staff/track files that will work with their board's "learning" features. After you have done it a few times, the procedure becomes fairly routine and goes rather quickly.
Good luck!