@Sam Abe this is a very common issue between owners and PMCs. 

Another possible option would be to do a cash out refinance to get some of my rehab money out of the property and only leave my 10-20% downpayment (whatever the HML lender requires to purchase the property)I would love to know if this is possible or if there are any issue with the plan, especially in the refinancing into a primary portion. 

You aren't doing much mechanical work on a house in Chicago in that price point with permits, etc. 

Most problems with Construction contracts and the resulting legal issues are due to the terms not being well defined in the beginning.Both parties need to know exactly what is expected of each other.

Look for any walls or areas of prior water issues, including the attic, roof, bathrooms.

If you ever plan to rehab the property and have to pull an electrical permit you could be required to do a complete rewire.

Then if he continues to bug you, bring up the driveway and ask if he wants to go down the route of the fence then you'll explore the driveway issue at the same time.

Your time is valuable, and if the buyers are serious, they should have no issue and realize this is standard.

Would I be able to issue a pay or vacate if she pays on the 2nd again? 

I'm holding onto my cash for any unseen issues..