Ninja could probably just be done as a Rogue with some changes to Everyman and Occupational skills and Profession bonuses. Less work than trying to do point conversions across the change in costing philosophies (skill-by-skill and thousands [okay, dozens] of variant professions tweaking skill costs v. by skill category and a standard system of Restricted/Everyman/Occupation for tweaking individual skill costs).
It's a shame you aren't using Training Packages, because they'd be great for doing Ninja with. You could also do Ninja as a culture if you're modeling the period where whole Ninja clans were resisting Samurai domination. In either case, you could then have Fighter Ninjas and Warrior Monk Ninjas for the more aggressive types, Thief Ninjas for the stealth-obsessed, Layman Ninjas who mainly work on creating all the great Ninja equipment, Monk Ninjas for the supernaturally-gifted Ninja, etc.