. -- You'll keep back maybe 5% of all rents for routine maintenance and another 5% for capX (big expenses like roof or furnace replacement).  

He had put pictures on the walls with nails and put a shelf/rack in the master bathroom which put holes in our walls.

You get SOME advantage of economy of scale on a 2-4 units like sharing the roof, one foundation, etc, however single family tenants are generally more caring of the house.

Is it ok to place metal roof over shingles?  

According to the inspection, a replacement job must be completed on the roof, windows, doors, siding, soffits, back deck, and front porch, to name a few (which one should I even start with?).

Even if, say, the roof needs replaced, but it isn't currently leaking and keeping you from renting the unit, then you can punt that option, at least for a bit.And I also second Rob's take on going straight to the contractors.  

Its a 3 unit row-house built 1900, pretty good condition, newer roof and water heaters, not sure of other stuff.

We believe the property could have been appraised for ~$115k (new medal roof, new HVAC, floors, fixtures, new sheet rock throughout).

Multi family is through the roof, as I'm sure it is in your area as well.

The building has been extensively renovated by the prior owners in 2022 including new heat/ac, appliances, flooring, kitchens/bathrooms, roof.