It's been two weeks since I got back from my trip and I thought I might share my experience since it might be helpful to others. I ended up taking the 5DmkII, a 580exII 24-70, 17-40, 135, and 85. The 24-70 was on the camera 90% of the time and the 135 and 85 shared 9%. I only used the 17-40 for a couple of shots. The flash never left the bag.
Because you have to walk everywhere in Japan and take public transit, the bag was actually quite heavy. Luckily I got used to the weight and all of the walking after the first couple of days.