Troubles with MIDI

I had a really hard time yesterday transcribing my Christ lag in Todesbanden, Op. 73 from MIDI to Sibelius notation. In the MIDI file that was generated from the Hauptwerk recording there are 3 tracks with 3 separate staves: all but the top track had every note that I played written in. The problem was that there seem to be no intelligent way to assign this music from one stave of MIDI to the 3 staves of organ score. I cleaned up the score with one plugin called Renotate Performance but everything else had to be done by hand. Creating this thing took me maybe 10 minutes but transcribing into Sibelius - entire day. I hope I can adjust some settings in Hauptwerk in the future so that less manual work would be needed.