I just started using GrandOrgue, but I have never found a solution to this problem:
Perhaps I'm mistaken, but I was under the impression that MIDI files for GrandOrgue (or Hauptwerk, for that matter) were supposed to be constructed so that MIDI track 1 is for Pedal, track2 for Great, track 3 for Swell, etc. I have a short organ piece I've been using for testing the sounds of different organs which has just 2 tracks: 1 for Pedal, and 2 for Great. However, it doesn't make any difference which organ I use: track 1 plays on the Swell (rather than Pedal), track 2 plays on the Great, and the Pedal doesn't play at all. On a 3-manual organ, track 1 still seems to be Swell (and perhaps Great, too, as the middle keyboard?), and track 2 might be Positive/Choir rather than Great. (It's hard to tell because it's sometimes difficult to tell which key outlines are matching the music.) In any case, the Pedal for sure is NOT playing.
This is quite frustrating. This MIDI issue also seems to be the area where I would like to see the greatest improvement in the User Manual. There seems to be very little information on setting up MIDI in GO (like, how about LOTS of examples!).
Help! And thanks in advance!
P.S. I use test: GrandOrgue-0.3.1.1928-117.8-win64.exe