However, they no longer have the property in their system due to release of mortgage.Any options when the bank owns the property? 

We've got 10 new ground up projects going right now. 

For example I reach out to my HVAC guy to get updates on pricing for mini splits, etc.

I would vote bookshelf, since in long term rentals, typically, you want the least amount of things you will need to fix, as possible.If short term rental, than Murphey bed would be my vote, typically.

I have another rental property that has suspended Passive Activity loss (that I decided to hold), can I use one property PAL to offset gain on sale for another? 

You are correct, that this has long been the conventional figure used to estimate cost for buildable sf in NYC. 

I’m curious to know—how do you approach your market research?

This would require seller to bring cash to closing.

Have them pay the repair company before closing with that much of your earnest money going hard in case you fail to close. 

Of course, this question is best posed to an attorney.