Hello John
Although I use a dismembered Yamaha keyboard to midify my pedals, the principle is the same - I use the remaining notes for my pistons. There is the issue that if you use the transposer you will "transpose" and therefore confuse your pistons, but as I never use it that's not a problem to me. In Hauptwerk you connect the organ pistons to the appropriate notes.
I also use momentary push button switches as the actual pistons. They're not quite as reliable or as easy to hit as real pistons, but they do work well.