Eddie- Your zoning classifications seem similar to ours (Commercial General, Industrial Light, etc) so I imagine your municipality used the same example ordinance when they adopted their zoning standards as mine did. It's a crappy ordinance, so I can see why the muni, and you, are having trouble with it. It's really designed for large-ish urban areas, not smaller rural towns. We've been amending ours almost constantly since we adopted it, because we keep finding things in it that don't work for our little town. I guess that's neither here nor there, but please try to remember that your guy you're talking to with your city has a crap hand to deal with with the ordinance he's enforcing.
If you wanted to build your building here, here's a snippet of what our zoning would require: Storage buildings are only permitted in the IL (Industrial Light) or IH (Industrial Heavy) zones. Engineered drawings and site plan required. Concrete, asphalt, or other "dust-free" parking required, which will come with a min. of parking spaces required depending on the size of the building (and don't forget to add 1 space for every required ADA space, because they take 2 spaces). Sidewalks required if on an undeveloped site. Stormwater management required. Screening requirements for dumpsters/outside storage. Lighting requirements for your parking lot. Sustainability requirements, design and façade requirements, etc, etc, etc. It's a decent sized ordeal to build a new building in town. And remember that if you rent out part of the building, it can only be rented to someone who's going to use their portion for a permitted use in the zone, so it'd have to be rented to someone who's also using it for storage, or for manufacturing, warehousing, transportation, or whatever else your town has permitted in that zone.
So that's a whole lot to say that boils down to, your city zoning isn't going to be cost-efficient for you to build a new building that you're not making money on. If I were you I'd either: A) buy an empty parcel in the county or somewhere outside of zoning restrictions or, B) buy a building that's already built that's close enough to what you want that you can make it work. Preferably, again, outside of a zoning jurisdiction.