So it is a pattern.....

I raised the lowered ceiling, leveled the sloping floor, added under the floor heating, a soaking tub and separate shower as well as high quality quartz tiling and glass shower with brass fixtures and double sink.

If that were the fact pattern and the prior owner had maintained a rental license, you would have been required to obtain a rental license  upon your purchase but the city would issue the license.

It sounds like you have set a pattern of simply doing what she wants.

Again, you should be able to put this into motion as long as you start a paper trail now, if you haven't done so already; you want accounts from different Tenants covering different instances in writing to show a pattern. 

just acquired a house for a rental that has Laminate wood flooring in the bedrooms and tile throughout the rest of the house.

Are there similar patterns in your neighborhood/will tenants/other prospective buyers care about this also?

However, based on your fact pattern, there will be a period of nonqualified use that will reduce the amount of the exclusion allowed.

We normally LVP kitchens with a stone/tile look, but in this case I wanted to have a wood look troughout the entire area.

Tile?