the stop numbers as presented by the player to the host are sequential from 1 to 120, and they don't map one-to-one onto the stop numbers shown in the player. For example, say I enable "stop 80" from my DAW - that actually maps onto stop 116, Soloflute 4' in the player.
So how does one figure out this mapping?
BTW, I also have Hauptwerk, which is marvelous: for the benefit of other posters it occupies an entirely different use case space, being a standalone program for those who want to emulate a pipe organ on a dedicated console and do nothing else. Churches who don't have millions of dollars for a pipe organ, and organists who want a convincing instrument at home are their main audience. Organ consoles that generate nothing but MIDI for Hauptwerk are available -- monster MIDI controllers! A supreme virtue of Hauptwerk is that sample sets from all manner of amazing instruments can be loaded into the program. They've provided a VST for connecting a DAW to it. With Hauptwerk you also have to program your own automation to manipulate stops (and pistons, etc.)