I had the same issues. I contacted Jake (subbas32) customhworgans@gmail.com, who created an extension. This odf mod applies the sostenuto to either the Choir/Accompanent manual or the Great manual. He added an Extension page to the odf where you can use Auto-detect to route these functions to the physical control switches you want to use. Really a very simple to use configuration. This feature can be added to any organ including classical sample sets. The file is very small and is added by means of Hauptwerk's organ Install
The Sostenuto itself is "connected" to the kick switch via a MIDI encoder input, where which manual it is applied to is controlled by one of the switches on the coupler rail. I came up with a circuit which uses a bi-color LED to indicate to which manual the Sostenuto is being applied. Blue for the lower manual, Green for the Great. The Sost routing can also be controlled via the combination action which also then shows up via the bi-color LED so you always know. Originally Jake set it up so that the manual routing feature was controlled by a maintained (SPDT) switch. I had him change it to be controlled by a momentary switch so that I could use my above circuit. Jake can provide it either way.
BTW, the cost was very reasonable.
Rgds,
Ed