The only fretless bass models to ever appear on the official Rickenbacker price sheets have been the 4001FL and the 4003FL. But back in the day when you could custom order some features (they don't do that anymore), you could get certain pickups, checker binding, special finishes, and trim items. Making a fretless bass is quite simple, just slap on a fretless fingerboard and make it fit. While working up the book, I found folks with fretless 4000, 4001S, 4002, 4003S, and 3001, none of which were listed as available. So how rare are they? No way to tell, but if this is only the second 4000 fretless that I've seen, there can't have been very many.
