OK, it sure does sound like you have a dead mouse in the ductwork somewhere. My condolences. If you can't see it from the registers or the furnace end, I'm not sure there's much that can be easily done to get it out.
We had a similar thing happen once growing up in our house (well, actually in the apartment above our garage, which was separate from the house). We taped off one register where it was most potent to attempt to keep the smell contained...with far from perfect success. It does improve over the course of a few weeks. I think the skeleton of the mouse was probably still there somewhere when the property was sold. We also rigged up a mousetrap with a length of wire attached so we could tether it to a register and stick down the duct in case we heard another one wandering around there, but I don't think we had need of using it.