PhotoNinja is just the work-horse RAW conversion package. However, in particular for recent work in IR false colour, I often merge PN output with results from ASP. Fuji false-colour IR is obtained with Bibble 4, which can run even under the various 64-bit operating systems, and has a synergetic relationship to these old RAF files, despite some stuff is lost in translation.
No matter from where the processed file originate, they end up in Photoshop for the final detail finish, any retouching, and scaling for archive storage.