Hello jeremalian,
I can't help you with Myco I'm afraid (we haven't tried that yet). However, in the Hauptwerk CODM organ definition format itself it's possible to do all of the things you mention. The CODM user's guide (on the Help menu in Hauptwerk) covers those things, and the format in general, in depth.
For example, swell boxes, the wind supply model (which needs the Advanced Edition of Hauptwerk) and key action noises are defined via the Division table. Stop, Coupler and Tremulant tables can also be used to define action noises for their corresponding objects.