When I resell the home do I just pay standard income tax or do I pay capital gains tax as well?

That's a huge prize in real estate investing, plus now we avoid the 3.8% healthcare tax as well that will hit ALL real estate investors, unless you or your spouse are full time.

That medicare tax as well will not be at that rate.

So if the IRA put down 60% and financed 40%, roughly 40% of the net income generated would be subject to this tax. As

Some states do not tax a property based on its condition.

There is no county property tax, as there is in most states.  

Is the New York City transfer tax a progressive tax?

Since you've removed the initial excess, only the gains are taxed (I'm guessing the IRS can't tax a contribution that never should have been there to begin with and is removed by the time you file).

Well, I am trying to figure why they would tax a buyer who takes out a mortgage and give tax preference to an all-cash buyer.

And I'm not doing anything hugely elaborate - just trying to figure out the best way to report income from a flip sale and avoid as much SE tax as I legally can.