Small world, I was in Tokyo with my 350D back in March/April of this year. If you are in Shinjuku, you've got to check out the Canon Digital Center there, it's caddy-corned across the street from the Hilton.
I have heard that some people have had to leave their cameras sit overnight with all batteries removed to clear them. Too bad you have to leave tomorrow. That is a really weird error. I take it that the error continues with a CF card in place. That's the only thing I can think of. Please keep us posted. I'm really wondering about the 40D, way too many issues around the world with this camera.
Even if your 40D isn't working, why not take it with you? If you are in Tokyo, Canon will work on your camera there while you wait. Their service was incredible when I was there. Don't worry if you don't speak Japanese, there will be someone there to help you.