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Rocky, I have done what you intend to do a number of time and second Bif's excellent advice. Among your focal lengths, I would leave out the 21. Japan is a crowded country, and opportunities for "clean" WA shots aren't that many. Ideally, I'd go with a 28/50 combo, but you don't have a 28, so 35 is "it" for wide angle. Then, if you have a 35 as go-everywhere walkabout lens, do you complement it with the 50 or the 90? That is a matter of what you want to shoot. The 50 would give you full coverage of "normal" shots alongside the 35, whereas the 90 would let you take more diverse shots, at the expense of a gap in between. Sure you can't handle 3?
Last piece of advice, Japan offers great opportunities for close-up photography, flowers, exquisite details etc... Make sure one of your two lenses covers that. Also, I'd never go without a tripod for night shots in Japanese cities. Even a table top one, if size and weight preclude a larger one can save the day!
Have fun, Japan is a country of inspiring beauty in so many ways...