If it applies to SFR, the SFR will be getting sold and removed from the rental market.  

You can void your contract because it only included 1 tenant/occupant and because a new spouse would not qualify had they been applying together based on his history and your acceptance criteria.

If 2 adults are applying (not married), do I run background/credit checks on both adults? 

You really need to talk to your tax guy to see how it applies since you live there part time.  

(We applied for a new construction permit and one of the steps was to ensure tree canopy was preserved to a certain percentage)The seller (previous owner) was the one who did the tree removal Tree removal was done prior to our lot acquisitionThe seller acknowledged that all fines and penalties were paid in line with the tree removal PRIOR to acquisition.

2nd, Depending on the smells, you may want to check certain parts of the house  and apply certain remedies.

It almost feels like I am out trying to get a loan;(   Ultimately, I am the customer and it is been a great experience when treated like one, I am pretty sure that since I am paying all the fees, points, environmental, appraisals- this puts me the position of "Customer"  most banks do not realize this and instead treat you like they are doing you a favor for even letting you apply.  

So my options are doing an FHA rehab loan, paying that off almost immediately and then applying for FHAFTB.

Growing your tool kit to apply to your business is priority in real estate.

Connect with a local investor, bring him deals, learn then apply what you learn, you are no ready  Good Luck