I deducted property-related expenses, such as mortgage interest, property taxes, and maintenance costs, from my taxable income.

We got a great deal on this property, it's positively cashed flowed over the past few years, we would actually profit on a refinance, and it'll carry an INF% return once refinanced according to the BRRRR calculator. 

There are calculators on this website, and more information on the website about how to do this mathematically.This is not a charity game .

Then I calculate that replacing the roof, HVAC, and remodeling bathrooms/kitchens would cost $400,000.  

And does your calculation take into consideration the fact that an entire town can burn down, and the only assistance the government will give you is a $700 gift card? 

If you don't have trusted professionals in the area you are looking at I think you should do some serious ROI calculations on the trips out there, the time developing the relationships, the time marketing and managing, etc.

I’m trying to value the property and believe its calculated by NOI/cap rate.

This is located in oak harbor WA on Whidbey Island if that is pertinent for calculating a deduction just a general idea would give me a huge help at least would be a starting point the rent is higher than a lot of similar apartments however as I stated it's on property but the lack of kitchen almost cancels out the benefit of the setting.

A homestead usually helps with lowering taxable value, but it's kind of screwing me over in this situation.

Selling for $1M with a $100k mortgage is not taxable, if you paid $1M for it.