When they renew, I do not charge anything additional.

Keep the insurance in the homeowners name (you become an additional insured), get a durable power of attorney from the homeowner, and make the payments on time!  

If you do sell within the next three years, you'll probably come out even, as you added the additional loan costs to the principal you need to pay down and your house will may be underwater (assuming you bought at market and there isn't crazy appreciation where you bought your house). 

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.

I'm technically newly self employed so I don't qualify for traditional financing through a mortgage company.

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.