That is not a small job for a first timer.

The amount increased will likely depend on your permit (i.e. architectural drawings or whatever).While the building inspector isn't specifically looking for code violations when inspecting the garage, it's a good idea not to have any obvious issues in plain view (for example, don't have an unpermitted kitchen rehab or HVAC install in progress when they inspect the garage and expect them to overlook it when they walk through the house!). 

Wet tiled area in the unit-like the kitchen floor?

I bought a “fourplex” where the 5th unit had been turned in to  “storage” (You know with a bathroom, kitchen, napping area...).

I understand that the major items like replacing floors, bath, kitchen, and HVAC will be depreciated over 27.5 years, but there are some items like scraping the ceiling, updating a drive way, and fixing a bathroom closet that I am not sure about.

First floor features living room with wood burning fireplace, formal dining room, kitchen with granite countertops, SS appliances, full bath with beautifully tiled shower, hardwood flooring and recessed lighting.

First floor features living room with wood burning fireplace, formal dining room, kitchen with granite countertops, SS appliances, full bath with beautifully tiled shower, hardwood flooring and recessed lighting.

Put an addition on the home, added a master suite, walk in pantry, half bathroom off the kitchen, built two car garage and split the lot of the home.

Even though I think she plans on being full time RE investor like I am, I want her to have that degree and life experience. 

I won't go into all of them, but the primary thing was that our kitchen cabinets were basically falling off the wall, the dishwasher stopped working after using it 3 times and the P-trap under the sink was malfunctioning, causing a constant water drip and massive hole under the sink - which they had covered up with a shelf and cleaning supplies.