I'd start by asking what camera bag you plan on using and are you fit enough to carry that bag everywhere? Do you plan on doing any traveling by rail while in Japan? That would limit the size of bag you can bring.
FWIW, my normal kit for a trip to Japan would be close to what you proposed: 17-40L, 24-70L, 35L, 135L, 1.4x TC, external flash.
If I'm going to take a lot of people shots, I'll bring the 85L too. My favorite two prime combo is the 35L and 85L. It's hard to resist to not bring it all --- I compromise by bringing a large/heavy camera bag on the plane and leave a lot of the gear in the hotel room.
Another option I have is to swap out the 17-40L for a Samyang/Rokinon 14/2.8.
My day bag is a Think Tank Retrospective 7 that I can manage to carry all day for about two weeks (I have worked out at the gym enough to be able to handle it for about that long). If I need more room while traveling by plane, I'll also bring a Think Tank Urban Disguise 60 II which holds everything, including my 14" laptop. These bags have excellent rain covers that clip to the bag strap so that you can quicly flip up the rain cover, get at your equipment, and gets stuff protected again --- works really well in heavy rain.
If I was *really* going to travel light, I'd go 24-70L, and a 35L. If I wanted more reach, swap out the 24-70L for a 24-105L or the Sigma version.
Other option for me is to go mirrorless (e.g. Fuji X100s, X-T1, 18-55, 55-200, 27/2.8, 35/1.4).