gamerprinter
Mapper/Publisher
Well, also looking at Pathfinder, I agree the Inquisitor is a good fit - use of divine spells and teamwork feats with an investigative flavor. Also looking at the Advanced Class Guide's new classes: investigator and slayer are also a good fit (both being hybrid classes combining rogue with alchemist on first, and with ranger on second).
For the organization, there are rules from Rite Publishing for the Kaidan setting of Japanese horror (PFRPG) for creating a Yakuza gang. I'd use that as a base, converting the Enterprises to secret police activities instead of yakuza ones - that's all you'd need to do to adapt to creating a secret police organization.
Upcoming from Kaidan will the Metsuki which is an archetype for inquisitor of exactly the Shogun's secret police.
For the organization, there are rules from Rite Publishing for the Kaidan setting of Japanese horror (PFRPG) for creating a Yakuza gang. I'd use that as a base, converting the Enterprises to secret police activities instead of yakuza ones - that's all you'd need to do to adapt to creating a secret police organization.
Upcoming from Kaidan will the Metsuki which is an archetype for inquisitor of exactly the Shogun's secret police.