If you are not Materially Participating, the loss will be reported on Form 8582 and like be classified as "Unallowed".The ordinary loss from Schedule E cannot offset the Schedule D capital gains. 

It is in fact taxed at much higher rate as ordinary income. 3.

I've also held of holding properties in individual LLCs that are owned by one S corporation, which allows for a 60 / 40 split between ordinary income (regular tax) and dividends (capital gains tax rate).With the goal of minimizing taxation and liability protection, what would be the recommendation from more experienced people here?

Congratulations, you get to share your partners tax burden and pay the depreciation recapture at ordinary income rates. 

Quote from @Melanie Baldridge: Why I like investing in real estate more than 401(k)s.Both offer tax deferrals, but here's the difference:If you're making pre-tax contributions to your 401(k), then withdrawals = ordinary income tax.With real estate gains, you're paying capital gains tax (which is typically lower).Plus, RE investors get:1.

In your case, changing the property from a rental to your primary residence constitutes a change in use.The depreciation recapture will be calculated based on the fair market value of the building at the time of conversion, not including the land value.Since you're tearing down the existing structure, the entire amount of depreciation taken over the past two years will likely be recaptured, as the building's value at conversion will effectively be zero.The recaptured amount will be taxed as ordinary income, up to a maximum rate of 25% for residential rental property (Section 1250 property).

@Tom Rairdon If you’ve owned your short-term rental (STR) for over a year, it likely qualifies for long-term capital gains (LTCG) treatment, taxed at lower rates (0%-20%) compared to your 33% ordinary income bracket.

The only thing that sounds out of the ordinary here is the water bill

You are allowed to charge for ALL damages beyond ordinary wear-and-tear.

There are several out there that I am aware of that are taxed at rates which are currently lower than ordinary income rates.