Hello Wolfman591,
Welcome to the forum.
I think your options would be:
1. Configure MIDI output from one of the sample set's existing virtual ranks (using "Organ settings | Advanced MIDI ... | Direct MIDI input/output for ranks/pipes", and probably also set that particular virtual rank not to be loaded (via "Organ | Load organ, adjusting rank ... options"). However, that would involve sacrificing a virtual rank, as you mentioned. Or:
2. Use the Custom Organ Design Module (CODM) to create your own organ definition from scratch.
3. If the organ definition isn't encrypted, you could perhaps see whether you could commission Jake (forum user subbas32) to create a customised, extended version of the existing organ definition for you:
https://forum.hauptwerk.com/viewtopic.php?f=6&t=20485