For a really Japanese experience one would create an entirely new system, but as none of us are likely to have that sort of time and energy, I would suggest that both Buddhism and Shinto be treated as Theistic. Much worship of local kami would be propitiatory in nature (thus needing no special rules). Sorcerors have been accounted for, but could also be allowed to worship the kami/bosatsu, unlike Glorantha. Time and occupational requirements should ensure that nobody gains unreasonable power (if there is such a thing)--sorcerors are not going to let any old samurai study their secrets.
The Buddhist mystics would be somewhat separated from the rest of society, as they were in reality, in monasteries. Certain warriors (such as Lone Wolf) may also lean this way, though it might be nice to differentiate samurai and fighting monks.
Perhaps you could look at LoN for its ideas on gaining magic through mass ceremonies, also the ki system (sorry, no specific ideas as all my books on Japn including LoN are about 3000 km away)
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