I just installed Wyre to make all my mods work and I have a couple questions (and will have more as I progress). What category would shops go into? This includes stuff like Lera & Pizz's shop and Apachii's shop.

probably in with quest mods... never used/looked at the BALO stuff, but that's where I'd put them as a default.... in some instances you may have to move them to a specific spot but that should be a good start.
Pacific Morrowind

This thing is going to put me in the funny farm...