It sounds like you're using classes from the Rokugan book and taint rules from the Oriental Adventures book? Because, unless I've overlooked something, Shugenja as printed in the Oriental Adventures book doesn't have multiclassing restrictions, and taint rules as printed in the Rokugan book don't give you taint for casting non-maho spells, even if you're in the shadowlands (and penalizes Cha, instead of Con and Wis).