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It's hard enough to find published low-level urban hack and slash--much less investigation-based adventures.
Streets of Zobeck is certainly worth mentioning. The Zobeck (Midgard) setting might give you what you want, but there's a lot of material to take in.
If you're going the Sherlock Holmes route instead of break-down-the-door-first-ask-questions-later approach, it might be easier just to pick a setting you like and grab a pdf detailing a major city. If you're comfortable using Golarion (default Pathfinder setting), there's:
Cities of Golarion - Contains write-ups on Cassomir (one of my favorite Golarion options), Corentyn, Ilizmagorti, Nisroch, Vigil, and Whitethrone.
City of Strangers - covers Kaer Maga (and this is just touching the surface)
Rule of Fear - Covers Ustalav regions, but doesn't focus on a single city like the previous two.
These are resources that I've used for urban investigation campaigns, but keep in mind that none of these three contain actual adventures. This route takes a bit of work, but if you can stay ahead of your players and adapt quickly go for it.
I've been debating about getting into Legendary Games' Gothic series; gothic horror tends to lean heavily on mystery so it might suit your needs.