Really interesting place. Couple of thoughts on your comments. The drop ceiling is unusual, as it has a decent looking drywall job above it. This is typically done when there is a need to meet fire codes, and a drop ceiling is a desired feature, as opposed to a typical drop ceiling that hides something ugly like exposed structure, or old crappy ceilings. Nothing odd in the wiring shown. some small, low voltage wire, possibly to a motion detector, and some 120 volt Romex, no biggy. Sadly, any sagging floors have nothing to do with hardwood or plywood. Sags are caused by inadequate structure, nothing more. In old buildings it is typically a combination of undersized floor joists, and damage to them over the years. It's common to find huge holes and notches in old framing, to accommodate plumbing, and other renovations. The solution is to repair and reinforce the joists, which can be a huge undertaking.
You might want to slow down and develop a good written outline of what you want to see as a finished product, and how you are going to get there. In some ways it's no different than building a new home, and there is a definite order of things, or chaos results. You give a few hints of this when discussing built-ins and hardwood, yet speak of plumbing issues. Issues pretty much need to be addressed in the order of structural repair/renovation, plumbing, HVAC, electrical, insulation , wall finishes, cabinets, etc..... You're further burdened by the fact that things like plumbing and sagging structure require access to the first floor, with some degree of ceiling and wall demolition, which is unlikely with a tenant in that space.
Great place, good luck with the renovations.