@Luke Bricca  I am or was a GC and can see about 20k coming into a simple remodeling project.

My tenant mentioned that there was a leak coming from the toilet in April.

No formula can be accurate across the board because even “cookie cutter” properties next store to each other differ as to view, location to the street, topography of the land, lot size, physical condition of the property, past remodeling, quality of the mechanical systems, sunlight, utility bills, past use, etc.  

So, I tried to help the situation by getting a contractor to go replace the floor and remodel the bathroom so that the house is nicer for her.

I'm sure your parents know what houses go for around them, is 413k for a new or freshly remodeled attainable there?

The tenant's sink and toilet in their only bathroom were under repair, and I want to know if the tenant has the right to withhold rent in this case, as the unit may not have been considered 'habitable' during that time.

Because of this, unsophisticated appraisers reduce as-is value more than they should.2nd, the appraiser estimates the increase of value, based on your remodel plan.

I remodeled complete rental myself.

They could put cement in the toilet, rocks down it, they could refuse to leave and leave you tied up for six months trying to get them out or more.

We added value by re-doing the whole house, installed vinyl floorings, rebuilt 2 and a half bathrooms, re-painted the whole house, replaced all the hardware in the house, installed new lighting, ceiling fans, re-painted the kitchen, and completely remodeled the upstairs.