Looking for something that helps factor in all variables, fixed costs, interest paid on hard money loans, reno costs, etc etc. 

Make sure you are asking about all the terms - the maturity date, the adjustment period, the costs, etc.  

However, I'm a bit confused about the process, specifically:Who is responsible for paying the closing costs, and how do you bring it up?

That certain company charges $700-1,000 just for setting up a basic LLC (mine cost $50 and took 20 minutes to set up so that’s a nice profit for that company) or up to $10,000 for a ridiculously over-complicated LLC structure with multiple LLC’s in different states that nobody would ever need that they try to upsell people on who don’t even own a single property yet. 

Size makes a big difference in cost.

This AC costs $17000 in 2020 and assume will no problem for a long time but most expensive one and shortest time died. 

For us in California the main metric is not "low cost".

Are there any red flags I should be aware of, such as the vacancy expense or NNN costs?

This process can be very costly, requires zoning permission, in addition to all the items you listed.

The property was originally set up to condo, but the area had declined and the property was a rental for 10 years or so.