I ran into a similar issue with a duplex brrrr in OKC last year, and the foundation company said it would only cost $2300 to make it right, so I pulled the trigger and bought it.

If it doesn't pass the appraisal than the FHA Amendatory Clause gets triggered.

My question is more about giving the properties a longer leash vs pulling the trigger to exchange them now.

I have read, that if the mortgage on your property is owned by Fannie Mae, then you are able to transfer your loan to an LLC without triggering the full repayment of the loan (https://servicing-guide.fannie...). 

Has anyone ever done a deal with the owner of a property? I have an option contract to protect me from the owner selling after I start renovations. Has anyone ever done a deal like this? Any recommendations. 

I've got my radar up for prospective properties and ready to pull the trigger should something come along.

This post is for the person that may be “thinking” about getting into REI, but is yet to pull the trigger on the first deal.

Sure don't waste their time by going to see lots of properties when you aren't ready to pull the trigger but they can set up alerts from the MLS so you get emails about new properties and can start to get a sense of the market.

Generally, this will not trigger transfer tax.  

They usually will have a percentage ownership that will trigger their guarantee requirement.