Then when you go to resell and pay additional costs you are taking a loss.

My question is should I have payed the $72,000 and but additional $15,000 in to the duplex and see if it cf at $87,000.

Borrower have some knowledge and experience in real estate investingI think your best bet is to find a seller where you can do either 1 or 2 above and honestly explain your situation, where you are financially now, and what you are trying to accomplish.  

I spell it out in my leases, such as the below: Additional appliances included at Property include: __refrigerator_____________________.

The seller disclosed the long term leases on two of the units, but only provided the expired, 2 year old lease and the rental increase notices for the other two  and did not produce the additional long term leases that tenants shared with me.I'm in a bind here, I can't break the leases and can't stay in compliance with the loan terms.I've already reached out to my agent, who is fortunately a commercial brokerage with an attorney on staff, but have not heard back.

I also bill at no additional charge for my GC work and bill everything at cost.

Don't worry about the inside/outside non-permit deal - that is something that could likely be done in a few days, and unless you are blatantly constructing (like a second floor addition) semi-long-term, the city probably won't notice.

.,  a title company may request additional information from previous owners. 

Normally if a client already owns a flagged hotel it would be some what easy to provide funding to buy an additional location.

Your best bet when it comes to HVAC is finding a reputable contractor through word of mouth.