FHA requires habitability, so broken windows will be a problem, leaking ceiling, obvious plumbing or electrical issues, etc. 

So it's just spelling out what the co-op commission is so we're all in the open and the seller understands that I am compensating the other agent fairly and not harming their chances at a solid offer by going cheap on the co-op fee. 

Observing the local habits of these folks.

My first step would be to refuse those two requests and offer to let him out of the lease "no harm, no foul", if he is not happy with the arrangement.  

The listing agent forwards me an inspection report that states the beam in subflooring shows signs of harmful water penetration and of termite damage.

I think you should be good on the setbacks and FAR because the property was built not too long ago and the plans show the same habitable space

was the property at least habitable and advertised to be rented?

Here is one I wrote, and you should read my other Blog posts too, and search all of BP.https://www.biggerpockets.com/blogs/10670/71992-education-and-mentoring-is-key-to-success-in-real-estate-investingHang in there, no harm done.

I thought I wanted to do live in fix and flips so I bought my first foreclosed house back in 2015 and have been living in it as soon as it was habitable and slowly finishing it off (emphasis on slowly, my Dad warned me I would never get it finished once I moved in!)

If so, is there a certificate of habitability?